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  • 1. Alonso-Mori, Roberto
    et al.
    Kern, Jan
    Gildea, Richard J
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Lassalle-Kaiser, Benedikt
    Tran, Rosalie
    Hattne, Johan
    Laksmono, Hartawan
    Hellmich, Julia
    Glöckner, Carina
    Echols, Nathaniel
    Sierra, Raymond G
    Schafer, Donald W
    Sellberg, Jonas
    Kenney, Christopher
    Herbst, Ryan
    Pines, Jack
    Hart, Philip
    Herrmann, Sven
    Grosse-Kunstleve, Ralf W
    Latimer, Matthew J
    Fry, Alan R
    Messerschmidt, Marc M
    Miahnahri, Alan
    Seibert, M Marvin
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025; .
    Zwart, Petrus H
    White, William E
    Adams, Paul D
    Bogan, Michael J
    Boutet, Sébastien
    Williams, Garth J
    Zouni, Athina
    Messinger, Johannes
    Glatzel, Pieter
    Sauter, Nicholas K
    Yachandra, Vittal K
    Yano, Junko
    Bergmann, Uwe
    Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 47, p. 19103-19107Article in journal (Refereed)
    Abstract [en]

    The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this "probe-before-destroy" approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kβ(1,3) XES spectra of Mn(II) and Mn(2)(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

  • 2.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca Stella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobicrajski, R.
    Tolcikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, no 1, p. 016403-Article in journal (Refereed)
    Abstract [en]

    Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 1017 W/cm2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 1016 W/cm2. This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.

  • 3. Aquila, Andrew
    et al.
    Hunter, Mark S.
    Doak, R. Bruce
    Kirian, Richard A.
    Fromme, Petra
    White, Thomas A.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Arnlund, David
    Bajt, Saša
    Barends, Thomas R. M.
    Barthelmess, Miriam
    Bogan, Michael J.
    Bostedt, Christoph
    Bottin, Hervé
    Bozek, John D.
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    DePonte, Daniel P.
    Elser, Veit
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Frank, Matthias
    Fromme, Raimund
    Graafsma, Heinz
    Grotjohann, Ingo
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y.
    Hartmann, Andreas
    Hartmann, Robert
    Hau-Riege, Stefan
    Hauser, Günter
    Hirsemann, Helmut
    Holl, Peter
    Holton, James M.
    Hömke, André
    Johansson, Linda
    Kimmel, Nils
    Kassemeyer, Stephan
    Krasniqi, Faton
    Kühnel, Kai-Uwe
    Liang, Mengning
    Lomb, Lukas
    Malmerberg, Erik
    Marchesini, Stefano
    Martin, Andrew V.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Messerschmidt, Marc
    Nass, Karol
    Reich, Christian
    Neutze, Richard
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schmidt, Carlo
    Schmidt, Kevin E.
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Soltau, Heike
    Shoeman, Robert L.
    Sierra, Raymond
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Strüder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wang, Xiaoyu
    Williams, Garth J.
    Weidenspointner, Georg
    Weierstall, Uwe
    Wunderer, Cornelia
    Barty, Anton
    Spence, John C. H.
    Chapman, Henry N.
    Time-resolved protein nanocrystallography using an X-ray free-electron laser2012In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, no 3, p. 2706-2716Article in journal (Refereed)
    Abstract [en]

    We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

  • 4. Arnlund, David
    et al.
    Johansson, Linda C
    Wickstrand, Cecilia
    Barty, Anton
    Williams, Garth J
    Malmerberg, Erik
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Milathianaki, Despina
    DePonte, Daniel P
    Shoeman, Robert L
    Wang, Dingjie
    James, Daniel
    Katona, Gergely
    Westenhoff, Sebastian
    White, Thomas A
    Aquila, Andrew
    Bari, Sadia
    Berntsen, Peter
    Bogan, Mike
    van Driel, Tim Brandt
    Doak, R Bruce
    Kjær, Kasper Skov
    Frank, Matthias
    Fromme, Raimund
    Grotjohann, Ingo
    Henning, Robert
    Hunter, Mark S
    Kirian, Richard A
    Kosheleva, Irina
    Kupitz, Christopher
    Liang, Mengning
    Martin, Andrew V
    Nielsen, Martin Meedom
    Messerschmidt, Marc
    Seibert, M Marvin
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA..
    Sjöhamn, Jennie
    Stellato, Francesco
    Weierstall, Uwe
    Zatsepin, Nadia A
    Spence, John C H
    Fromme, Petra
    Schlichting, Ilme
    Boutet, Sébastien
    Groenhof, Gerrit
    Chapman, Henry N
    Neutze, Richard
    Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 9, p. 923-926Article in journal (Refereed)
    Abstract [en]

    We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.

  • 5. Barty, Anton
    et al.
    Boutet, Sebastien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Bogan, Michael J.
    Hau-Riege, Stefan
    Marchesini, Stefano
    Sokolowski-Tinten, Klaus
    Stojanovic, Nikola
    Tobey, Ra'Anan
    Ehrke, Henri
    Cavalleri, Andrea
    Duesterer, Stefan
    Frank, Matthias
    Bajt, Sasa
    Woods, Bruce W.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Treusch, Rolf
    Chapman, Henry N.
    Ultrafast single-shot diffraction imaging of nanoscale dynamics2008In: Nature Photonics, ISSN 1749-4885, Vol. 2, no 7, p. 415-419Article in journal (Refereed)
    Abstract [en]

    The transient nanoscale dynamics of materials on femtosecond to picosecond timescales is of great interest in the study of condensed phase dynamics such as crack formation, phase separation and nucleation, and rapid fluctuations in the liquid state or in biologically relevant environments. The ability to take images in a single shot is the key to studying non-repetitive behaviour mechanisms, a capability that is of great importance in many of these problems. Using coherent diffraction imaging with femtosecond X-ray free-electron-laser pulses we capture time-series snapshots of a solid as it evolves on the ultrafast timescale. Artificial structures imprinted on a Si3N4 window are excited with an optical laser and undergo laser ablation, which is imaged with a spatial resolution of 50 nm and a temporal resolution of 10 ps. By using the shortest available free-electron-laser wavelengths(1) and proven synchronization methods(2) this technique could be extended to spatial resolutions of a few nanometres and temporal resolutions of a few tens of femtoseconds. This experiment opens the door to a new regime of time-resolved experiments in mesoscopic dynamics.

  • 6. Barty, Anton
    et al.
    Caleman, Carl
    Aquila, Andrew
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lomb, Lukas
    White, Thomas A.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Arnlund, David
    Bajt, Sasa
    Barends, Thomas R. M.
    Barthelmess, Miriam
    Bogan, Michael J.
    Bostedt, Christoph
    Bozek, John D.
    Coffee, Ryan
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    DePonte, Daniel P.
    Doak, R. Bruce
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Elser, Veit
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Fromme, Petra
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y.
    Hartmann, Robert
    Hartmann, Andreas
    Hauser, Guenter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S.
    Johansson, Linda
    Kassemeyer, Stephan
    Kimmel, Nils
    Kirian, Richard A.
    Liang, Mengning
    Maia, Filipe R. N. C.
    Malmerberg, Erik
    Marchesini, Stefano
    Martin, Andrew V.
    Nass, Karol
    Neutze, Richard
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Scott, Howard
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shoeman, Robert L.
    Sierra, Raymond G.
    Soltau, Heike
    Spence, John C. H.
    Stellato, Francesco
    Stern, Stephan
    Strueder, Lothar
    Ullrich, Joachim
    Wang, X.
    Weidenspointner, Georg
    Weierstall, Uwe
    Wunderer, Cornelia B.
    Chapman, Henry N.
    Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements2012In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 6, no 1, p. 35-40Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis(1). For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information(1-4). Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology(5) should enable structural determination from submicrometre protein crystals with atomic resolution.

  • 7.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gunn, Laura H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Flueckiger, Leonie
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lundholm, Ida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kulyk, Olena
    Higashiura, Akifumi
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Ne-Te Duane
    Wysong, Taylor E.
    Bostedt, Christoph
    Gorkhover, Tais
    Iwan, Bianca
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Osipov, Timur
    Walter, Peter
    Hart, Philip
    Bucher, Maximilian
    Ulmer, Anatoli
    Ray, Dipanwita
    Carini, Gabriella
    Ferguson, Ken R.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Electrospray sample injection for single-particle imaging with x-ray lasers2019In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed)
  • 8. Bogan, M. J.
    et al.
    Boutet, S.
    Barty, A.
    Benner, W. H.
    Frank, M.
    Lomb, L.
    Shoeman, R.
    Starodub, D.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S. P.
    Woods, B.
    Decorwin-Martin, P.
    Bajt, S.
    Schulz, J.
    Rohner, U.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, S.
    Schlichting, I.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, H. N.
    Single-shot femtosecond x-ray diffraction from randomly oriented ellipsoidal nanoparticles2010In: Physical Review Special Topics. Accelerators and Beams, ISSN 1098-4402, E-ISSN 1098-4402, Vol. 13, no 9, p. 094701-Article in journal (Refereed)
    Abstract [en]

    Coherent diffractive imaging of single particles using the single-shot "diffract and destroy" approach with an x-ray free electron laser (FEL) was recently demonstrated. A high-resolution low-noise coherent diffraction pattern, representative of the object before it turns into a plasma and explodes, results from the interaction of the FEL with the particle. Iterative phase retrieval algorithms are used to reconstruct two-dimensional projection images of the object from the recorded intensities alone. Here we describe the first single-shot diffraction data set that mimics the data proposed for obtaining 3D structure from identical particles. Ellipsoidal iron oxide nanoparticles (250 nm x 50 nm) were aerosolized and injected through an aerodynamic lens stack into a soft x-ray FEL. Particle orientation was not controlled with this injection method. We observed that, at the instant the x-ray pulse interacts with the particle, a snapshot of the particle's orientation is encoded in the diffraction pattern. The results give credence to one of the technical concepts of imaging individual nanometer and subnanometer-sized objects such as single molecules or larger clusters of molecules using hard x-ray FELs and will be used to help develop robust algorithms for determining particle orientations and 3D structure.

  • 9. Bogan, Michael J
    et al.
    Benner, W Henry
    Boutet, Sébastien
    Rohner, Urs
    Frank, Matthias
    Barty, Anton
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, Stefano
    Bajt, Sasa
    Woods, Bruce
    Riot, Vincent
    Hau-Riege, Stefan P
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Spiller, Eberhard
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N
    Single particle X-ray diffractive imaging2008In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 8, no 1, p. 310-6Article in journal (Refereed)
    Abstract [en]

    In nanotechnology, strategies for the creation and manipulation of nanoparticles in the gas phase are critically important for surface modification and substrate-free characterization. Recent coherent diffractive imaging with intense femtosecond X-ray pulses has verified the capability of single-shot imaging of nanoscale objects at suboptical resolutions beyond the radiation-induced damage threshold. By intercepting electrospray-generated particles with a single 15 femtosecond soft-X-ray pulse, we demonstrate diffractive imaging of a nanoscale specimen in free flight for the first time, an important step toward imaging uncrystallized biomolecules.

  • 10. Bogan, Michael J.
    et al.
    Boutet, Sebastien
    Chapman, Henry N.
    Marchesini, Stefano
    Barty, Anton
    Benner, W. Henry
    Rohner, Urs
    Frank, Matthias
    Hau-Riege, Stefan P.
    Bajt, Sasa
    Woods, Bruce
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schulz, Joachim
    Aerosol Imaging with a Soft X-Ray Free Electron Laser2010In: Aerosol Science and Technology, ISSN 0278-6826, E-ISSN 1521-7388, Vol. 44, no 3, p. I-VIArticle in journal (Refereed)
    Abstract [en]

    Lasers have long played a critical role in the advancement of aerosol science. A new regime of ultrafast laser technology has recently be realized, the world's first soft x-ray free electron laser. The Free electron LASer in Hamburg, FLASH, user facility produces a steady source of 10 femtosecond pulses of 7–32 nm x-rays with 1012 photons per pulse. The high brightness, short wavelength, and high repetition rate (> 500 pulses per second) of this laser offers unique capabilities for aerosol characterization. Here we use FLASH to perform the highest resolution imaging of single PM2.5 aerosol particles in flight to date. We resolve to 35 nm the morphology of fibrous and aggregated spherical carbonaceous nanoparticles that existed for less than two milliseconds in vacuum. Our result opens the possibility for high spatial- and time-resolved single particle aerosol dynamics studies, filling a critical technological need in aerosol science.

  • 11.
    Boutet, Sebastien
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Bogan, Michael J.
    Barty, Anton
    Frank, Matthias
    Benner, W. Henry
    Marchesini, Stefano
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Chapman, Henry N.
    Ultrafast soft X-ray scattering and reference-enhanced diffractive imaging of weakly scattering nanoparticles2008In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 166, p. 65-73Article in journal (Refereed)
    Abstract [en]

    We report the first successful reconstruction of the real space image from coherent X-ray diffraction patterns of membrane-supported nanoparticles using single ultrafast pulses. The particles consisted of 145-nm spherical polystyrene spheres that were size-selected by differential mobility analysis. We investigated the dependence of signal intensity on the number of spherical nanoparticles irradiated by single ultrafast pulses at the FLASH FEL facility. We demonstrate detection of as few as two 145-nm diameter particles irradiated by a single 32 nm fs-long FLASH pulse focused to 2.4Jcm(-2). In this case the noise in the diffraction pattern. due to photon-counting statistics and scattering from the supporting silicon nitride membrane, was the largest contributor to the recorded intensity. We were able to reconstruct high-resolution images of the nanoparticles using a strong scattering reference object to aid the phase retrieval of the coherent diffraction pattern. This method of reference-enhanced diffractive imaging may allow the imaging of weakly scattering objects at FLASH and other future X-ray FEL sources.

  • 12. Boutet, Sébastien
    et al.
    Lomb, Lukas
    Williams, Garth J
    Barends, Thomas R M
    Aquila, Andrew
    Doak, R Bruce
    Weierstall, Uwe
    DePonte, Daniel P
    Steinbrener, Jan
    Shoeman, Robert L
    Messerschmidt, Marc
    Barty, Anton
    White, Thomas A
    Kassemeyer, Stephan
    Kirian, Richard A
    Seibert, M Marvin
    Montanez, Paul A
    Kenney, Chris
    Herbst, Ryan
    Hart, Philip
    Pines, Jack
    Haller, Gunther
    Gruner, Sol M
    Philipp, Hugh T
    Tate, Mark W
    Hromalik, Marianne
    Koerner, Lucas J
    van Bakel, Niels
    Morse, John
    Ghonsalves, Wilfred
    Arnlund, David
    Bogan, Michael J
    Caleman, Carl
    Fromme, Raimund
    Hampton, Christina Y
    Hunter, Mark S
    Johansson, Linda C
    Katona, Gergely
    Kupitz, Christopher
    Liang, Mengning
    Martin, Andrew V
    Nass, Karol
    Redecke, Lars
    Stellato, Francesco
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, Dingjie
    Zatsepin, Nadia A
    Schafer, Donald
    Defever, James
    Neutze, Richard
    Fromme, Petra
    Spence, John C H
    Chapman, Henry N
    Schlichting, Ilme
    High-resolution protein structure determination by serial femtosecond crystallography2012In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 337, no 6092, p. 362-364Article in journal (Refereed)
    Abstract [en]

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  • 13. Chapman, H N
    et al.
    Bajt, S
    Barty, A
    Benner, W H
    Bogan, M J
    Boutet, S
    Cavalleri, A
    Duesterer, S
    Frank, M
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S P
    Iwan, B
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, S
    Sakdinawat, A
    Sokolowski-Tinten, K
    Seibert, Marvin M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Treusch, R
    Woods, B W
    Coherent imaging at FLASH2009In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 186, no 1, p. 012051-Article in journal (Refereed)
    Abstract [en]

    We have carried out high-resolution single-pulse coherent diffractive imaging at the FLASH free-electron laser. The intense focused FEL pulse gives a high-resolution low-noise coherent diffraction pattern of an object before that object turns into a plasma and explodes. In particular we are developing imaging of biological specimens beyond conventional radiation damage resolution limits, developing imaging of ultrafast processes, and testing methods to characterize and perform single-particle imaging.

  • 14. Chapman, Henry N.
    et al.
    Barty, Anton
    Bogan, Michael J.
    Boutet, Sebastien
    Frank, Matthias
    Hau-Riege, Stefan P.
    Marchesini, Stefano
    Woods, Bruce W.
    Bajt, Sasa
    Benner, Henry
    London, Richard A.
    Ploenjes, Elke
    Kuhlmann, Marion
    Treusch, Rolf
    Duesterer, Stefan
    Tschentscher, Thomas
    Schneider, Jochen R.
    Spiller, Eberhard
    Moeller, Thomas
    Bostedt, Christoph
    Hoener, Matthias
    Shapiro, David A.
    Hodgson, Keith O.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Lee, Richard W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Szöke, Abraham
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär Biofysik.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär Biofysik.
    Femtosecond diffractive imaging with a soft-X-ray free-electron laser2006In: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 2, no 12, p. 839-843Article in journal (Refereed)
    Abstract [en]

    Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).

  • 15. Chapman, Henry N.
    et al.
    Fromme, Petra
    Barty, Anton
    White, Thomas A.
    Kirian, Richard A.
    Aquila, Andrew
    Hunter, Mark S.
    Schulz, Joachim
    DePonte, Daniel P.
    Weierstall, Uwe
    Doak, R. Bruce
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Schlichting, Ilme
    Lomb, Lukas
    Coppola, Nicola
    Shoeman, Robert L.
    Epp, Sascha W.
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Holl, Peter
    Liang, Mengning
    Barthelmess, Miriam
    Caleman, Carl
    Boutet, Sebastien
    Bogan, Michael J.
    Krzywinski, Jacek
    Bostedt, Christoph
    Bajt, Sasa
    Gumprecht, Lars
    Rudek, Benedikt
    Erk, Benjamin
    Schmidt, Carlo
    Hoemke, Andre
    Reich, Christian
    Pietschner, Daniel
    Strueder, Lothar
    Hauser, Guenter
    Gorke, Hubert
    Ullrich, Joachim
    Herrmann, Sven
    Schaller, Gerhard
    Schopper, Florian
    Soltau, Heike
    Kuehnel, Kai-Uwe
    Messerschmidt, Marc
    Bozek, John D.
    Hau-Riege, Stefan P.
    Frank, Matthias
    Hampton, Christina Y.
    Sierra, Raymond G.
    Starodub, Dmitri
    Williams, Garth J.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rocker, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Stern, Stephan
    Nass, Karol
    Andritschke, Robert
    Schroeter, Claus-Dieter
    Krasniqi, Faton
    Bott, Mario
    Schmidt, Kevin E.
    Wang, Xiaoyu
    Grotjohann, Ingo
    Holton, James M.
    Barends, Thomas R. M.
    Neutze, Richard
    Marchesini, Stefano
    Fromme, Raimund
    Schorb, Sebastian
    Rupp, Daniela
    Adolph, Marcus
    Gorkhover, Tais
    Andersson, Inger
    SLU.
    Hirsemann, Helmut
    Potdevin, Guillaume
    Graafsma, Heinz
    Nilsson, Björn
    Spence, John C. H.
    Femtosecond X-ray protein nanocrystallography2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 470, no 7332, p. 73-77Article in journal (Refereed)
    Abstract [en]

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source(4). We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes(5). More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (similar to 200 nm to 2 mm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes(6). This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  • 16. Chapman, Henry N
    et al.
    Hau-Riege, Stefan P
    Bogan, Michael J
    Bajt, Sasa
    Barty, Anton
    Boutet, Sébastien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, Stefano
    Frank, Matthias
    Woods, Bruce W
    Benner, W Henry
    London, Richard A
    Rohner, Urs
    Szöke, Abraham
    Spiller, Eberhard
    Möller, Thomas
    Bostedt, Christoph
    Shapiro, David A
    Kuhlmann, Marion
    Treusch, Rolf
    Plönjes, Elke
    Burmeister, Florian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Femtosecond time-delay X-ray holography2007In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 448, no 7154, p. 676-679Article in journal (Refereed)
    Abstract [en]

    Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment1, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging2, 3 can be used to achieve high resolution, beyond radiation damage limits for biological samples4. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.

  • 17.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Benner, W. Henry
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tîmneanu, Nicuşor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ekeberg, Tomas
    Loh, N. Duane
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kirian, Richard A.
    Awel, Salah
    Wiedorn, Max O.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastian
    Williams, Garth
    Koglin, Jason
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed)
  • 18.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Claverie, Jean-Michel
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Chapman, Henry
    Bostedt, Christoph
    Bozek, John D.
    Ferguson, Ken R.
    Krzywinski, Jacek
    Epp, Sascha W.
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Kimmel, Nils
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser2015In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, p. 098102:1-6, article id 098102Article in journal (Refereed)
  • 19.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Aquila, Andrew
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Ctr Etud Saclay, Commissariat Energie Atom & Energies Alternat, F-91191 Gif Sur Yvette, France..
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Liang, Meng
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Martin, Andrew V.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Melbourne, 161 Barry St, Melbourne, Vic 3010, Australia..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Bajt, Sasa
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barthelmess, Miriam
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Coppola, Nicola
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Claverie, Jean-Michel
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Loh, N. Duane
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;Natl Univ Singapore, Ctr BioImaging Sci, 14 Sci Dr 4 Blk S1 A, Singapore 117546, Singapore..
    Bostedt, Christoph
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bozek, John D.
    Synchrotron SOLEIL, Lorme Merisiers Roundabout St Aubin, F-91190 St Aubin, France..
    Krzywinski, Jacek
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bogan, Michael J.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Hampton, Christina Y.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Sierra, Raymond G.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Frank, Matthias
    Lawrence Livermore Natl Lab, 7000 East Ave,Mail Stop L-211, Livermore, CA 94551 USA..
    Shoeman, Robert L.
    Lomb, Lukas
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Foucar, Lutz
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Epp, Sascha W.
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Rolles, Daniel
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Rudenko, Artem
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Hartmann, Robert
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Hartmann, Andreas
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Kimmel, Nils
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Holl, Peter
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Weidenspointner, Georg
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Rudek, Benedikt
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Erk, Benjamin
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Kassemeyer, Stephan
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Schlichting, Ilme
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Strueder, Lothar
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany.;Univ Siegen, Emmy Noether Campus,Walter Flex Str 3, D-57068 Siegen, Germany..
    Ullrich, Joachim
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Phys Tech Bundesanstalt, Bundesallee 100, D-38116 Braunschweig, Germany..
    Schmidt, Carlo
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Krasniqi, Faton
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Hauser, Guenter
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Reich, Christian
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Soltau, Heike
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Schorb, Sebastian
    Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany..
    Hirsemann, Helmut
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Wunderer, Cornelia
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Graafsma, Heinz
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Notkestr 85, D-22607 Hamburg, Germany..
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160060Article in journal (Refereed)
    Abstract [en]

    Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

  • 20. Frank, Matthias
    et al.
    Carlson, David B
    Hunter, Mark S
    Williams, Garth J
    Messerschmidt, Marc
    Zatsepin, Nadia A
    Barty, Anton
    Benner, W Henry
    Chu, Kaiqin
    Graf, Alexander T
    Hau-Riege, Stefan P
    Kirian, Richard A
    Padeste, Celestino
    Pardini, Tommaso
    Pedrini, Bill
    Segelke, Brent
    Seibert, M Marvin
    Linac Coherent Light Source, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
    Spence, John C H
    Tsai, Ching-Ju
    Lane, Stephen M
    Li, Xiao-Dan
    Schertler, Gebhard
    Boutet, Sebastien
    Coleman, Matthew
    Evans, James E
    Femtosecond X-ray diffraction from two-dimensional protein crystals2014In: IUCrJ, ISSN 2052-2525, Vol. 1, no 2, p. 95-100Article in journal (Refereed)
    Abstract [en]

    X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

  • 21. Fuchs, M.a b
    et al.
    Trigo, M.b c
    Chen, J.b
    Ghimire, S.b
    Shwartz, S.d
    Kozina, M.b
    Jiang, M.b
    Henighan, T.b
    Bray, C.b
    Ndabashimiye, G.b
    Feng, Y.e
    Herrmann, S.f
    Carini, G.f
    Pines, J.f
    Hart, P.f
    Kenney, C.f
    Guillet, S.e
    Boutete, Sébastien
    Williams, G.e
    Messerschmidt, M.e
    Seibert, M. M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Möllere, Stefan
    Hastings, J.B.e
    Reis, D.A.b g
    Nonlinear X-ray compton scattering2014Conference paper (Other academic)
    Abstract [en]

    We use XFEL pulses to observe the most fundamental nonlinear X-ray-matter interaction: nonlinear Compton scattering. In contrast to theoretical predictions, we measure an anonymous and yet to be explained red-shift in the observed photon energy.

  • 22. Gorkhover, Tais
    et al.
    Ulmer, Anatoli
    Ferguson, Ken
    Bucher, Max
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Bruza, Petr
    Carron, Sebastian
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Krzywinski, Jacek
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Morgan, Andrew
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Müller, Maria
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rupp, Daniela
    Sauppe, Mario
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Swiggers, Michelle
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Williams, Garth
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N.
    Faigel, Gyula
    Möller, Thomas
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bostedt, Christoph
    Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles2018In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 12, p. 150-153Article in journal (Refereed)
  • 23.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Uetrecht, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Bari, Sadia
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Epp, Sascha W.
    Chapman, Henry N.
    Barty, Anton
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    A data set from flash X-ray imaging of carboxysomes2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed)
    Abstract [en]

    Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

  • 24.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gijs, van der Schot
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha
    Chapman, Henry N.
    Barty, Anton
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    High-throughput imaging of heterogeneous cell organelles with an X-ray laser2014In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 8, no 12, p. 943-949Article in journal (Refereed)
    Abstract [en]

    We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.

  • 25. Hattne, Johan
    et al.
    Echols, Nathaniel
    Tran, Rosalie
    Kern, Jan
    Gildea, Richard J
    Brewster, Aaron S
    Alonso-Mori, Roberto
    Glöckner, Carina
    Hellmich, Julia
    Laksmono, Hartawan
    Sierra, Raymond G
    Lassalle-Kaiser, Benedikt
    Lampe, Alyssa
    Han, Guangye
    Gul, Sheraz
    DiFiore, Dörte
    Milathianaki, Despina
    Fry, Alan R
    Miahnahri, Alan
    White, William E
    Schafer, Donald W
    Seibert, M Marvin
    Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA.
    Koglin, Jason E
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Sellberg, Jonas
    Latimer, Matthew J
    Glatzel, Pieter
    Zwart, Petrus H
    Grosse-Kunstleve, Ralf W
    Bogan, Michael J
    Messerschmidt, Marc
    Williams, Garth J
    Boutet, Sébastien
    Messinger, Johannes
    Zouni, Athina
    Yano, Junko
    Bergmann, Uwe
    Yachandra, Vittal K
    Adams, Paul D
    Sauter, Nicholas K
    Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 5, p. 545-548Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

  • 26. Hau-Riege, Stefan P.
    et al.
    Boutet, Sebastien
    Barty, Anton
    Bajt, Sasa
    Bogan, Michael J.
    Frank, Matthias
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sakdinawat, Anne
    Schulz, Joachim
    Treusch, Rolf
    Chapman, Henry N.
    Sacrificial Tamper Slows Down Sample Explosion in FLASH Diffraction Experiments2010In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 104, no 6, p. 064801-Article in journal (Refereed)
    Abstract [en]

    Intense and ultrashort x-ray pulses from free-electron lasers open up the possibility for near-atomic resolution imaging without the need for crystallization. Such experiments require high photon fluences and pulses shorter than the time to destroy the sample. We describe results with a new femtosecond pump-probe diffraction technique employing coherent 0.1 keV x rays from the FLASH soft x-ray free-electron laser. We show that the lifetime of a nanostructured sample can be extended to several picoseconds by a tamper layer to dampen and quench the sample explosion, making <1 nm resolution imaging feasible.

  • 27. Hunter, Mark S
    et al.
    Segelke, Brent
    Messerschmidt, Marc
    Williams, Garth J
    Zatsepin, Nadia A
    Barty, Anton
    Benner, W Henry
    Carlson, David B
    Coleman, Matthew
    Graf, Alexander
    Hau-Riege, Stefan P
    Pardini, Tommaso
    Seibert, M Marvin
    Evans, James
    Boutet, Sébastien
    Frank, Matthias
    Fixed-target protein serial microcrystallography with an x-ray free electron laser.2014In: Scientific reports, ISSN 2045-2322, Vol. 4, p. 6026-Article in journal (Refereed)
    Abstract [en]

    We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.

  • 28.
    Iwan, Bianca S
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobierajski, R.
    Toleikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    TOF-OFF: A method for determining focal positions in tightly focused free-electron laser experiments by measurement of ejected ions2011In: High Energy Density Physics, ISSN 1574-1818, Vol. 7, no 4, p. 336-342Article in journal (Refereed)
    Abstract [en]

    Pulse intensities greater than 1017 Watt/cm2 were reached at the FLASH soft X-ray laser in Hamburg, Germany, using an off-axis parabolic mirror to focus 15 fs pulses of 5–70 μJ energy at 13.5 nm wavelength to a micron-sized spot. We describe the interaction of such pulses with niobium and vanadium targets and their deuterides. The beam produced craters in the solid targets, and we measured the kinetic energy of ions ejected from these craters. Ions with several keV kinetic energy were observed from craters approaching 5 μm in depth when the sample was at best focus. We also observed the onset of saturation in both ion acceleration and ablation with pulse intensities exceeding 1016 W/cm2, when the highest detected ion energies and the crater depths tend to saturate with increasing intensity.

    A general difficulty in working with micron and sub-micron focusing optics is finding the exact focus of the beam inside a vacuum chamber. Here we propose a direct method to measure the focal position to a resolution better than the Rayleigh length. The method is based on the correlation between the energies of ejected ions and the physical dimensions of the craters. We find that the focus position can be quickly determined from the ion time-of-flight (TOF) data as the target is scanned through the expected focal region. The method does not require external access to the sample or venting the vacuum chamber. Profile fitting employed to analyze the TOF data can extend resolution beyond the actual scanning step size.

  • 29. Johansson, Linda C.
    et al.
    Arnlund, David
    Katona, Gergely
    White, Thomas A.
    Barty, Anton
    DePonte, Daniel P.
    Shoeman, Robert L.
    Wickstrand, Cecilia
    Sharma, Amit
    Williams, Garth J.
    Aquila, Andrew
    Bogan, Michael J.
    Caleman, Carl
    Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Doak, R. Bruce
    Frank, Matthias
    Fromme, Raimund
    Galli, Lorenzo
    Grotjohann, Ingo
    Hunter, Mark S.
    Kassemeyer, Stephan
    Kirian, Richard A.
    Kupitz, Christopher
    Liang, Mengning
    Lomb, Lukas
    Malmerberg, Erik
    Martin, Andrew V.
    Messerschmidt, Marc
    Nass, Karol
    Redecke, Lars
    Seibert, M. Marvin
    Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA.
    Sjoehamn, Jennie
    Steinbrener, Jan
    Stellato, Francesco
    Wang, Dingjie
    Wahlgren, Weixaio Y.
    Weierstall, Uwe
    Westenhoff, Sebastian
    Zatsepin, Nadia A.
    Boutet, Sebastien
    Spence, John C. H.
    Schlichting, Ilme
    Chapman, Henry N.
    Fromme, Petra
    Neutze, Richard
    Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, no Article nr:2911Article in journal (Refereed)
    Abstract [en]

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 angstrom resolution and determine its serial femtosecond crystallography structure to 3.5 angstrom resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

  • 30. Johansson, Linda C
    et al.
    Arnlund, David
    White, Thomas A
    Katona, Gergely
    DePonte, Daniel P
    Weierstall, Uwe
    Doak, R Bruce
    Shoeman, Robert L
    Lomb, Lukas
    Malmerberg, Erik
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Nass, Karol
    Liang, Mengning
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Bozek, John D
    Caleman, Carl
    Coffee, Ryan
    Coppola, Nicola
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y
    Hartmann, Robert
    Hartmann, Andreas
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S
    Kassemeyer, Stephan
    Kimmel, Nils
    Kirian, Richard A
    Maia, Filipe R N C
    Marchesini, Stefano
    Martin, Andrew V
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sierra, Raymond G
    Soltau, Heike
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Struder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wahlgren, Weixiao Y
    Wang, Xiaoyu
    Weidenspointner, Georg
    Wunderer, Cornelia
    Fromme, Petra
    Chapman, Henry N
    Spence, John C H
    Neutze, Richard
    Lipidic phase membrane protein serial femtosecond crystallography2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 3, p. 263-265Article in journal (Refereed)
    Abstract [en]

    X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.

  • 31. Kern, Jan
    et al.
    Alonso-Mori, Roberto
    Hellmich, Julia
    Tran, Rosalie
    Hattne, Johan
    Laksmono, Hartawan
    Glöckner, Carina
    Echols, Nathaniel
    Sierra, Raymond G
    Sellberg, Jonas
    Lassalle-Kaiser, Benedikt
    Gildea, Richard J
    Glatzel, Pieter
    Grosse-Kunstleve, Ralf W
    Latimer, Matthew J
    McQueen, Trevor A
    DiFiore, Dörte
    Fry, Alan R
    Messerschmidt, Marc
    Miahnahri, Alan
    Schafer, Donald W
    Seibert, M Marvin
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025.
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Zwart, Petrus H
    White, William E
    Adams, Paul D
    Bogan, Michael J
    Boutet, Sébastien
    Williams, Garth J
    Messinger, Johannes
    Sauter, Nicholas K
    Zouni, Athina
    Bergmann, Uwe
    Yano, Junko
    Yachandra, Vittal K
    Room temperature femtosecond X-ray diffraction of photosystem II microcrystals2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 25, p. 9721-9726Article in journal (Refereed)
    Abstract [en]

    Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.

  • 32. Kern, Jan
    et al.
    Alonso-Mori, Roberto
    Tran, Rosalie
    Hattne, Johan
    Gildea, Richard J
    Echols, Nathaniel
    Glöckner, Carina
    Hellmich, Julia
    Laksmono, Hartawan
    Sierra, Raymond G
    Lassalle-Kaiser, Benedikt
    Koroidov, Sergey
    Lampe, Alyssa
    Han, Guangye
    Gul, Sheraz
    Difiore, Dörte
    Milathianaki, Despina
    Fry, Alan R
    Miahnahri, Alan
    Schafer, Donald W
    Messerschmidt, Marc
    Seibert, M Marvin
    Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA..
    Koglin, Jason E
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Sellberg, Jonas
    Latimer, Matthew J
    Grosse-Kunstleve, Ralf W
    Zwart, Petrus H
    White, William E
    Glatzel, Pieter
    Adams, Paul D
    Bogan, Michael J
    Williams, Garth J
    Boutet, Sébastien
    Messinger, Johannes
    Zouni, Athina
    Sauter, Nicholas K
    Yachandra, Vittal K
    Bergmann, Uwe
    Yano, Junko
    Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 340, no 6131, p. 491-495Article in journal (Refereed)
    Abstract [en]

    Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

  • 33. Kern, Jan
    et al.
    Tran, Rosalie
    Alonso-Mori, Roberto
    Koroidov, Sergey
    Echols, Nathaniel
    Hattne, Johan
    Ibrahim, Mohamed
    Gul, Sheraz
    Laksmono, Hartawan
    Sierra, Raymond G
    Gildea, Richard J
    Han, Guangye
    Hellmich, Julia
    Lassalle-Kaiser, Benedikt
    Chatterjee, Ruchira
    Brewster, Aaron S
    Stan, Claudiu A
    Glöckner, Carina
    Lampe, Alyssa
    DiFiore, Dörte
    Milathianaki, Despina
    Fry, Alan R
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Koglin, Jason E
    Gallo, Erik
    Uhlig, Jens
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Zwart, Petrus H
    Skinner, David E
    Bogan, Michael J
    Messerschmidt, Marc
    Glatzel, Pieter
    Williams, Garth J
    Boutet, Sébastien
    Adams, Paul D
    Zouni, Athina
    Messinger, Johannes
    Sauter, Nicholas K
    Bergmann, Uwe
    Yano, Junko
    Yachandra, Vittal K
    Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4371-Article in journal (Refereed)
    Abstract [en]

    The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

  • 34. Koopmann, Rudolf
    et al.
    Cupelli, Karolina
    Redecke, Lars
    Nass, Karol
    DePonte, Daniel P
    White, Thomas A
    Stellato, Francesco
    Rehders, Dirk
    Liang, Mengning
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Boutet, Sebastien
    Bozek, John D
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Doak, R Bruce
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y
    Hartmann, Andreas
    Hartmann, Robert
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S
    Kassemeyer, Stephan
    Kirian, Richard A
    Lomb, Lukas
    Maia, Filipe R N C
    Kimmel, Nils
    Martin, Andrew V
    Messerschmidt, Marc
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shoeman, Robert L
    Sierra, Raymond G
    Soltau, Heike
    Stern, Stephan
    Struder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wang, Xiaoyu
    Weidenspointner, Georg
    Weierstall, Uwe
    Williams, Garth J
    Wunderer, Cornelia B
    Fromme, Petra
    Spence, John C H
    Stehle, Thilo
    Chapman, Henry N
    Betzel, Christian
    Duszenko, Michael
    In vivo protein crystallization opens new routes in structural biology2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 3, p. 259-262Article in journal (Refereed)
    Abstract [en]

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

  • 35. Kupitz, Christopher
    et al.
    Basu, Shibom
    Grotjohann, Ingo
    Fromme, Raimund
    Zatsepin, Nadia A
    Rendek, Kimberly N
    Hunter, Mark S
    Shoeman, Robert L
    White, Thomas A
    Wang, Dingjie
    James, Daniel
    Yang, Jay-How
    Cobb, Danielle E
    Reeder, Brenda
    Sierra, Raymond G
    Liu, Haiguang
    Barty, Anton
    Aquila, Andrew L
    Deponte, Daniel
    Kirian, Richard A
    Bari, Sadia
    Bergkamp, Jesse J
    Beyerlein, Kenneth R
    Bogan, Michael J
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Chao, Tzu-Chiao
    Conrad, Chelsie E
    Davis, Katherine M
    Fleckenstein, Holger
    Galli, Lorenzo
    Hau-Riege, Stefan P
    Kassemeyer, Stephan
    Laksmono, Hartawan
    Liang, Mengning
    Lomb, Lukas
    Marchesini, Stefano
    Martin, Andrew V
    Messerschmidt, Marc
    Milathianaki, Despina
    Nass, Karol
    Ros, Alexandra
    Roy-Chowdhury, Shatabdi
    Schmidt, Kevin
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Steinbrener, Jan
    Stellato, Francesco
    Yan, Lifen
    Yoon, Chunhong
    Moore, Thomas A
    Moore, Ana L
    Pushkar, Yulia
    Williams, Garth J
    Boutet, Sébastien
    Doak, R Bruce
    Weierstall, Uwe
    Frank, Matthias
    Chapman, Henry N
    Spence, John C H
    Fromme, Petra
    Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 513, no 7517, p. 261-265Article in journal (Refereed)
    Abstract [en]

    Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

  • 36. Lee, Ho-Hsien
    et al.
    Cherni, Irene
    Yu, HongQi
    Fromme, Raimund
    Doran, Jeffrey D.
    Grotjohann, Ingo
    Mittman, Michele
    Basu, Shibom
    Deb, Arpan
    Dörner, Katerina
    Aquila, Andrew
    Barty, Anton
    Boutet, Sébastien
    Chapman, Henry N.
    Doak, R. Bruce
    Hunter, Mark S.
    James, Daniel
    Kirian, Richard A.
    Kupitz, Christopher
    Lawrence, Robert M.
    Liu, Haiguang
    Nass, Karol
    Schlichting, Ilme
    Schmidt, Kevin E.
    Seibert, M. Marvin
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA,.
    Shoeman, Robert L.
    Spence, John C. H.
    Stellato, Francesco
    Weierstall, Uwe
    Williams, Garth J.
    Yoon, Chunhong
    Wang, Dingjie
    Zatsepin, Nadia A.
    Hogue, Brenda G.
    Matoba, Nobuyuki
    Fromme, Petra
    Mor, Tsafrir S.
    Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-12014In: IUCrJ, ISSN 2052-2525, Vol. 1, no 5, p. 305-317Article in journal (Refereed)
    Abstract [en]

    CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) andthe membrane-proximal region of gp41 (MPR), the transmembrane envelopeprotein ofHuman immunodeficiency virus 1(HIV-1), and has previously beenshown to induce the production of anti-HIV-1 antibodies with antiviralfunctions. To further improve the design of this candidate vaccine, X-raycrystallography experiments were performed to obtain structural informationabout this fusion protein. Several variants of CTB-MPR were designed,constructed and recombinantly expressed inEscherichia coli. The first variantcontained a flexible GPGP linker between CTB and MPR, and yielded crystalsthat diffracted to a resolution of 2.3 A ̊, but only the CTB region was detectedin the electron-density map. A second variant, in which the CTB was directlyattached to MPR, was shown to destabilize pentamer formation. A thirdconstruct containing a polyalanine linker between CTB and MPR proved tostabilize the pentameric form of the protein during purification. The purificationprocedure was shown to produce a homogeneously pure and monodispersesample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered inthe third dimension. Nanocrystals obtained using the same precipitant showedpromising X-ray diffraction to 5 A ̊resolution in femtosecond nanocrystallo-graphy experiments at the Linac Coherent Light Source at the SLAC NationalAccelerator Laboratory. The results demonstrate the utility of femtosecondX-ray crystallography to enable structural analysis based on nano/microcrystalsof a protein for which no macroscopic crystals ordered in three dimensions havebeen observed before.

  • 37. Liu, Wei
    et al.
    Wacker, Daniel
    Gati, Cornelius
    Han, Gye Won
    James, Daniel
    Wang, Dingjie
    Nelson, Garrett
    Weierstall, Uwe
    Katritch, Vsevolod
    Barty, Anton
    Zatsepin, Nadia A.
    Li, Dianfan
    Messerschmidt, Marc
    Boutet, Sebastien
    Williams, Garth J.
    Koglin, Jason E.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, Chong
    Shah, Syed T. A.
    Basu, Shibom
    Fromme, Raimund
    Kupitz, Christopher
    Rendek, Kimberley N.
    Grotjohann, Ingo
    Fromme, Petra
    Kirian, Richard A.
    Beyerlein, Kenneth R.
    White, Thomas A.
    Chapman, Henry N.
    Caffrey, Martin
    Spence, John C. H.
    Stevens, Raymond C.
    Cherezov, Vadim
    Serial Femtosecond Crystallography of G Protein-Coupled Receptors2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 342, no 6165, p. 1521-1524Article in journal (Refereed)
    Abstract [en]

    X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.

  • 38. Loh, N. D.
    et al.
    Bogan, M. J.
    Elser, V.
    Barty, A.
    Boutet, S.
    Bajt, S.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schulz, J.
    Seibert, Marvin Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, S.
    Schlichting, I.
    Shoeman, R. L.
    Lomb, L.
    Frank, M.
    Liang, M.
    Chapman, H. N.
    Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns2010In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 104, no 22, p. 225501-1-225501-5Article in journal (Refereed)
    Abstract [en]

    We reconstructed the 3D Fourier intensity distribution of monodisperse prolate nanoparticles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast x-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the expansion-maximization-compression framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.

  • 39. Lomb, Lukas
    et al.
    Barends, Thomas R. M.
    Kassemeyer, Stephan
    Aquila, Andrew
    Epp, Sascha W.
    Erk, Benjamin
    Foucar, Lutz
    Hartmann, Robert
    Rudek, Benedikt
    Rolles, Daniel
    Rudenko, Artem
    Shoeman, Robert L.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J.
    Bostedt, Christoph
    Bozek, John D.
    Caleman, Carl
    Coffee, Ryan
    Coppola, Nicola
    DePonte, Daniel P.
    Doak, R. Bruce
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, Holger
    Fromme, Petra
    Gebhardt, Maike
    Graafsma, Heinz
    Gumprecht, Lars
    Hampton, Christina Y.
    Hartmann, Andreas
    Hauser, Guenter
    Hirsemann, Helmut
    Holl, Peter
    Holton, James M.
    Hunter, Mark S.
    Kabsch, Wolfgang
    Kimmel, Nils
    Kirian, Richard A.
    Liang, Mengning
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Meinhart, Anton
    Marchesini, Stefano
    Martin, Andrew V.
    Nass, Karol
    Reich, Christian
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sierra, Raymond
    Soltau, Heike
    Spence, John C. H.
    Steinbrener, Jan
    Stellato, Francesco
    Stern, Stephan
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, Xiaoyu
    Weidenspointner, Georg
    Weierstall, Uwe
    White, Thomas A.
    Wunderer, Cornelia
    Chapman, Henry N.
    Ullrich, Joachim
    Strüder, Lothar
    Schlichting, Ilme
    Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser2011In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 84, no 21, p. 214111-1-214111-6Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.

  • 40.
    Lundholm, Ida V.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bruza, Petr
    Bucher, Max
    Carron, Sebastian
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ferguson, Ken
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Krzywinski, Jacek
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Morgan, Andrew
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Müller, Maria
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rupp, Daniela
    Sauppe, Mario
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Swiggers, Michelle
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ulmer, Anatoli
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Williams, Garth
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Faigel, Gyula
    Chapman, Henry N.
    Möller, Thomas
    Bostedt, Christoph
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gorkhover, Tais
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging2018In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed)
  • 41. Marchesini, Stefano
    et al.
    Boutet, Sebastien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Sakdinawat, Anne E.
    Bogan, Michael J.
    Bajt, Sasa
    Barty, Anton
    Chapman, Henry N.
    Frank, Matthias
    Hau-Riege, Stefan P.
    Szoeke, Abraham
    Cui, Congwu
    Shapiro, David A.
    Howells, Malcolm R.
    Spence, John C. H.
    Shaevitz, Joshua W.
    Lee, Joanna Y.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Massively parallel X-ray holography2008In: Nature Photonics, ISSN 1749-4885, Vol. 2, no 9, p. 560-563Article in journal (Refereed)
    Abstract [en]

    Advances in the development of free-electron lasers offer the realistic prospect of nanoscale imaging on the timescale of atomic motions. We identify X-ray Fourier-transform holography(1,2,3) as a promising but, so far, inefficient scheme to do this. We show that a uniformly redundant array(4) placed next to the sample, multiplies the efficiency of X-ray Fourier transform holography by more than three orders of magnitude, approaching that of a perfect lens, and provides holographic images with both amplitude-and phase-contrast information. The experiments reported here demonstrate this concept by imaging a nano-fabricated object at a synchrotron source, and a bacterial cell with a soft-X-ray free-electron laser, where illumination by a single 15-fs pulse was successfully used in producing the holographic image. As X-ray lasers move to shorter wavelengths we expect to obtain higher spatial resolution ultrafast movies of transient states of matter.

  • 42. Milathianaki, D.
    et al.
    Boutet, S.
    Williams, G. J.
    Higginbotham, A.
    Ratner, D.
    Gleason, A. E.
    Messerschmidt, M.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA. .
    Swift, D. C.
    Hering, P.
    Robinson, J.
    White, W. E.
    Wark, J. S.
    Femtosecond Visualization of Lattice Dynamics in Shock-Compressed Matter2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 342, no 6155, p. 220-223Article in journal (Refereed)
    Abstract [en]

    The ultrafast evolution of microstructure is key to understanding high-pressure and strain-rate phenomena. However, the visualization of lattice dynamics at scales commensurate with those of atomistic simulations has been challenging. Here, we report femtosecond x-ray diffraction measurements unveiling the response of copper to laser shock-compression at peak normal elastic stresses of similar to 73 gigapascals (GPa) and strain rates of 10(9) per second. We capture the evolution of the lattice from a one-dimensional (1D) elastic to a 3D plastically relaxed state within a few tens of picoseconds, after reaching shear stresses of 18 GPa. Our in situ high-precision measurement of material strength at spatial (<1 micrometer) and temporal (<50 picoseconds) scales provides a direct comparison with multimillion-atom molecular dynamics simulations.

  • 43.
    Munke, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Bean, Richard J.
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    Bucher, Maximilian
    Chapman, Henry N.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Elser, Veit
    Fromme, Petra
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Higashiura, Akifumi
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lan, Ti-Yen
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liu, Haiguang
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nakagawa, Atsushi
    Nam, Daewoong
    Nelson, Garrett
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ourmazd, Abbas
    Rose, Max
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schwander, Peter
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Sierra, Raymond G.
    Song, Changyong
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Vartanyants, Ivan A.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wiedorn, Max O.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Yoon, Chun Hong
    Zook, James
    Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed)
  • 44.
    Novotny, Marian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Kleywegt, Gerard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    On the precision of calculated solvent-accessible surface areas2007In: Acta Crystallographica Section D: Biological Crystallography, ISSN 0907-4449, E-ISSN 1399-0047, Vol. 63, no 2, p. 270-274Article in journal (Refereed)
    Abstract [en]

    The fact that protein structures are dynamic by nature and that structure models determined by X-ray crystallography, electron microscopy (EM) and nuclear magnetic resonance (NMR) spectroscopy have limited accuracy limits the precision with which derived properties can be reported. Here, the issue of the precision of calculated solvent-accessible surface areas (ASAs) is addressed. A number of protein structures of different sizes were selected and the effect of random shifts applied to the atomic coordinates on ASA values was investigated. Standard deviations of the ASA calculations were found to range from ∼10 to ∼80  Å2. Similar values are obtained for a handful of cases in the Protein Data Bank (PDB) where `ensembles' of crystal structures were refined against the same data set. The ASA values for 69 hen egg-white lysozyme structures were calculated and a standard deviation of the ASA of 81  Å2 was obtained (the average ASA value was 6571  Å2). The calculated ASA values do not show any correlation with factors such as resolution or overall temperature factors. A molecular-dynamics (MD) trajectory of lysozyme was also analysed. The ASA values during the simulation covered a range of more than 800  Å2. If different programs are used, the ASA values obtained for one small protein show a spread of almost 600  Å2. These results suggest that in most cases reporting ASA values with a precision better than 10  Å2 is probably not realistic and a precision of 50–100  Å2 would seem prudent. The precision of buried surface-area calculations for complexes is also discussed.

  • 45.
    Popp, David
    et al.
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Loh, N. Duane
    Natl Univ Singapore, Dept Phys, Singapore 117557, Singapore.;Natl Univ Singapore, Ctr BioImaging Sci, Singapore 117546, Singapore..
    Zorgati, Habiba
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.;Natl Univ Singapore, Dept Biochem, Singapore 117597, Singapore..
    Ghoshdastider, Umesh
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Liow, Lu Ting
    Natl Univ Singapore, Dept Med, Singapore 119074, Singapore..
    Ivanova, Magdalena I.
    Univ Michigan, Dept Neurol, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA..
    Larsson, Mårten
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bean, Richard
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;European XFEL GmbH, D-22761 Hamburg, Germany..
    Beyerlein, Kenneth R.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Gati, Cornelius
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Oberthuer, Dominik
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Inst Biochem & Mol Biol, D-22607 Hamburg, Germany..
    Arnlund, David
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Branden, Gisela
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Berntsen, Peter
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Cascio, Duilio
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Chavas, Leonard M. G.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chen, Joe P. J.
    Univ Canterbury, Computat Imaging Grp, Dept Elect & Comp Engn, Christchurch, New Zealand.;Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Ding, Ke
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Harimoorthy, Rajiv
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Mossou, Estelle
    Inst Laue Langevin, F-38000 Grenoble, France.;Keele Univ, EPSAM ISTM, Keele ST5 5BG, Staffs, England..
    Sawaya, Michael R.
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Brewster, Aaron S.
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA..
    Hattne, Johan
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA.;Howard Hughes Med Inst, Janelia Res Campus,19700 Helix Dr, Ashburn, VA 20147 USA..
    Sauter, Nicholas K.
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA..
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seuring, Carolin
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Stellato, Francesco
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Tilp, Thomas
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Eisenberg, David S.
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Williams, Garth J.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Koglin, Jason E.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Makowski, Lee
    Northeastern Univ, Dept Bioengn, 360 Huntington Ave, Boston, MA 02115 USA..
    Millane, Rick P.
    Univ Canterbury, Computat Imaging Grp, Dept Elect & Comp Engn, Christchurch, New Zealand..
    Forsyth, Trevor
    Inst Laue Langevin, F-38000 Grenoble, France.;Keele Univ, EPSAM ISTM, Keele ST5 5BG, Staffs, England..
    Boutet, Sebastien
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    White, Thomas A.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22607 Hamburg, Germany..
    Chen, Swaine L.
    Natl Univ Singapore, Dept Med, Singapore 119074, Singapore.;ASTAR, Biopolis, Genome Inst Singapore, Singapore 138672, Singapore..
    Liang, Mengning
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Neutze, Richard
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Robinson, Robert C.
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.;Natl Univ Singapore, Dept Biochem, Singapore 117597, Singapore.;Okayama Univ, Res Inst Interdisciplinary Sci, Okayama 7008530, Japan..
    Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser2017In: CYTOSKELETON, ISSN 1949-3584, Vol. 74, no 12, p. 472-481Article in journal (Refereed)
    Abstract [en]

    A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked -strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual -synuclein amyloids.

  • 46.
    Rath, Asawari D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, Holger
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    Kirian, Richard
    Bean, Richard
    Barty, Anton
    Galli, Lorenzo
    Nass, Karol
    Barthelmess, Miriam
    Aquila, Andrew
    Toleikis, Sven
    Treusch, Rolf
    Roling, Sebastian
    Wöstmann, Michael
    Zacharias, Helmut
    Chapman, Henry N.
    Bajt, Saša
    DePonte, Daniel
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser2014In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 23, p. 28914-28925Article in journal (Refereed)
    Abstract [en]

    We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 1016 W/cm2 with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.

  • 47.
    Reddy, Hemanth K. N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Yoon, Chun Hong
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bobkov, Sergey
    Bucher, Maximilian
    Carini, Gabriella A.
    Carron, Sebastian
    Chapman, Henry
    Daurer, Benedikt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fromme, Petra
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hart, Philip
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Kurta, Ruslan P.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nam, Daewoong
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ourmazd, Abbas
    Rose, Max
    Schwander, Peter
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Song, Changyong
    Spence, John C. H.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed)
  • 48. Redecke, Lars
    et al.
    Nass, Karol
    Deponte, Daniel P
    White, Thomas A
    Rehders, Dirk
    Barty, Anton
    Stellato, Francesco
    Liang, Mengning
    Barends, Thomas R M
    Boutet, Sébastien
    Williams, Garth J
    Messerschmidt, Marc
    Seibert, M Marvin
    Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA. .
    Aquila, Andrew
    Arnlund, David
    Bajt, Sasa
    Barth, Torsten
    Bogan, Michael J
    Caleman, Carl
    Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany. .
    Chao, Tzu-Chiao
    Doak, R Bruce
    Fleckenstein, Holger
    Frank, Matthias
    Fromme, Raimund
    Galli, Lorenzo
    Grotjohann, Ingo
    Hunter, Mark S
    Johansson, Linda C
    Kassemeyer, Stephan
    Katona, Gergely
    Kirian, Richard A
    Koopmann, Rudolf
    Kupitz, Chris
    Lomb, Lukas
    Martin, Andrew V
    Mogk, Stefan
    Neutze, Richard
    Shoeman, Robert L
    Steinbrener, Jan
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, Dingjie
    Weierstall, Uwe
    Zatsepin, Nadia A
    Spence, John C H
    Fromme, Petra
    Schlichting, Ilme
    Duszenko, Michael
    Betzel, Christian
    Chapman, Henry N
    Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 339, no 6116, p. 227-230Article in journal (Refereed)
    Abstract [en]

    The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtain the room-temperature 2.1 Å resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction before destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.

  • 49.
    Ryan, Rebecca A.
    et al.
    Univ Melbourne, Sch Phys, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic, Australia..
    Williams, Sophie
    Univ Melbourne, Sch Phys, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic, Australia..
    Martin, Andrew V.
    Univ Melbourne, Sch Phys, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic, Australia..
    Dilanian, Ruben A.
    Univ Melbourne, Sch Phys, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic, Australia..
    Darmanin, Connie
    La Trobe Univ, Australian Res Council, Ctr Excellence Adv Mol Imaging, Dept Chem & Phys,La Trobe Inst Mol Sci, Bundoora, Vic, Australia..
    Putkunz, Corey T.
    Univ Melbourne, Sch Phys, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic, Australia..
    Wood, David
    Imperial Coll London, Dept Phys, London, England..
    Streltsov, Victor A.
    Florey Inst Neurosci & Mental Hlth, Parkville, Vic, Australia..
    Jones, Michael W. M.
    Queensland Univ Technol, Sci & Engn Fac, Brisbane, Qld, Australia..
    Gaffney, Naylyn
    Swinburne Univ Technol, Hawthorn, Vic, Australia..
    Hofmann, Felix
    Univ Oxford, Dept Engn Sci, Oxford, England..
    Williams, Garth J.
    Brookhaven Natl Lab, Upton, NY 11973 USA..
    Boutet, Sebastien
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA USA..
    Messerschmidt, Marc
    BioXFEL Sci & Technol Ctr, Buffalo, NY USA..
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Curwood, Evan K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Balaur, Eugeniu
    La Trobe Univ, Australian Res Council, Ctr Excellence Adv Mol Imaging, Dept Chem & Phys,La Trobe Inst Mol Sci, Bundoora, Vic, Australia..
    Peele, Andrew G.
    Nugent, Keith A.
    La Trobe Univ, Australian Res Council, Ctr Excellence Adv Mol Imaging, Dept Chem & Phys,La Trobe Inst Mol Sci, Bundoora, Vic, Australia..
    Quiney, Harry M.
    Univ Melbourne, Sch Phys, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic, Australia..
    Abbey, Brian
    La Trobe Univ, Australian Res Council, Ctr Excellence Adv Mol Imaging, Dept Chem & Phys,La Trobe Inst Mol Sci, Bundoora, Vic, Australia..
    Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene2017In: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, no 126, article id e56296Article in journal (Refereed)
    Abstract [en]

    The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C-60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C-60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.

  • 50.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Flexibility of scaffolded DNA origamiManuscript (preprint) (Other academic)
12 1 - 50 of 66
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