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Ekeberg, Tomas
Publications (10 of 31) Show all publications
Morgan, A. J., Ayyer, K., Barty, A., Chen, J. P. J., Ekeberg, T., Oberthuer, D., . . . Chapman, H. N. (2019). Ab initio phasing of the diffraction of crystals with translational disorder. ACTA CRYSTALLOGRAPHICA A: FOUNDATION AND ADVANCES, 75, 25-40
Open this publication in new window or tab >>Ab initio phasing of the diffraction of crystals with translational disorder
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2019 (English)In: ACTA CRYSTALLOGRAPHICA A: FOUNDATION AND ADVANCES, ISSN 2053-2733, Vol. 75, p. 25-40Article in journal (Refereed) Published
Abstract [en]

To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protein is refined against the set of observed Bragg reflections from a protein crystal. The resolution of the refined protein structure is limited by the highest angle at which Bragg reflections can be observed. In addition, the Bragg reflections alone are typically insufficient (by a factor of two) to determine the structure ab initio, and so prior information is required. Crystals formed from an imperfect packing of the protein molecules may also exhibit continuous diffraction between and beyond these Bragg reflections. When this is due to random displacements of the molecules from each crystal lattice site, the continuous diffraction provides the necessary information to determine the protein structure without prior knowledge, to a resolution that is not limited by the angular extent of the observed Bragg reflections but instead by that of the diffraction as a whole. This article presents an iterative projection algorithm that simultaneously uses the continuous diffraction as well as the Bragg reflections for the determination of protein structures. The viability of this method is demonstrated on simulated crystal diffraction.

Place, publisher, year, edition, pages
INT UNION CRYSTALLOGRAPHY, 2019
Keywords
X-ray diffraction, diffuse scattering, phase retrieval, macromolecular crystallography
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-373306 (URN)10.1107/S2053273318015395 (DOI)000454255400004 ()30575581 (PubMedID)
Available from: 2019-01-16 Created: 2019-01-16 Last updated: 2019-01-16Bibliographically approved
Lundholm, I. V., Sellberg, J. A., Ekeberg, T., Hantke, M. F., Okamoto, K., van der Schot, G., . . . Maia, F. R. N. (2018). Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. IUCrJ, 5, 531-541
Open this publication in new window or tab >>Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
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2018 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-360034 (URN)10.1107/S2052252518010047 (DOI)000444010100003 ()
Projects
eSSENCE
Available from: 2018-09-01 Created: 2018-09-09 Last updated: 2019-07-01Bibliographically approved
Gorkhover, T., Ulmer, A., Ferguson, K., Bucher, M., Maia, F. R. N., Bielecki, J., . . . Bostedt, C. (2018). Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles [Letter to the editor]. Nature Photonics, 12, 150-153
Open this publication in new window or tab >>Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles
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2018 (English)In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 12, p. 150-153Article in journal, Letter (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-345590 (URN)10.1038/s41566-018-0110-y (DOI)000426153800014 ()
Projects
eSSENCE
Available from: 2018-02-26 Created: 2018-03-09 Last updated: 2019-07-01Bibliographically approved
Östlin, C., Timneanu, N., Jönsson, H. O., Ekeberg, T., Martin, A. V. & Caleman, C. (2018). Reproducibility of Single Protein Explosions Induced by X-ray Lasers. Physical Chemistry, Chemical Physics - PCCP, 20(18), 12381-12389
Open this publication in new window or tab >>Reproducibility of Single Protein Explosions Induced by X-ray Lasers
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2018 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 18, p. 12381-12389Article in journal (Refereed) Published
Abstract [en]

Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems – four polypeptides with different amounts of surface bound water – were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.

Keywords
XFEL, Single-particle imaging, Coulomb explosion, ultrafast, GROMACS, simulation.
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-329340 (URN)10.1039/C7CP07267H (DOI)000431825300006 ()
Funder
Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research Carl Tryggers foundation
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2019-04-28Bibliographically approved
Reddy, H. K. N., Yoon, C. H., Aquila, A., Awel, S., Ayyer, K., Barty, A., . . . Xavier Paulraj, L. (2017). Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source. Scientific Data, 4, Article ID 170079.
Open this publication in new window or tab >>Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source
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2017 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-328536 (URN)10.1038/sdata.2017.79 (DOI)000404232100001 ()28654088 (PubMedID)
Projects
eSSENCE
Available from: 2017-06-27 Created: 2017-08-25 Last updated: 2019-08-25Bibliographically approved
Sala, S., Daurer, B. J., Hantke, M. F., Ekeberg, T., Loh, N. D., Maia, F. R. N. & Thibault, P. (2017). Ptychographic imaging for the characterization of X-ray free-electron laser beams. In: Rau, C (Ed.), X-RAY MICROSCOPY CONFERENCE 2016 (XRM 2016): . Paper presented at 13th International X-Ray Microscopy Conference (XRM), AUG 15-19, 2016, Diamond Light Source, Oxford, ENGLAND. , Article ID 012032.
Open this publication in new window or tab >>Ptychographic imaging for the characterization of X-ray free-electron laser beams
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2017 (English)In: X-RAY MICROSCOPY CONFERENCE 2016 (XRM 2016) / [ed] Rau, C, 2017, article id 012032Conference paper, Published paper (Refereed)
Abstract [en]

We present some preliminary results from a study aimed at the characterization of the wavefront of X-ray free electron laser (XFEL) beams in the same operation conditions as for single particle imaging (or flash X-ray imaging) experiments. The varying illumination produced by wavefront fluctuations between several pulses leads to a partially coherent average beam which can be decomposed into several coherent modes using ptychographic reconstruction algorithms. Such a decomposition can give insight into pulse-to-pulse variations of the wavefront. We discuss data collected at the Linac Coherent Light Source (LCLS) and FERMI.

Series
Journal of Physics Conference Series, ISSN 1742-6588 ; 849
National Category
Medical Image Processing
Identifiers
urn:nbn:se:uu:diva-346768 (URN)10.1088/1742-6596/849/1/012032 (DOI)000412800900032 ()
Conference
13th International X-Ray Microscopy Conference (XRM), AUG 15-19, 2016, Diamond Light Source, Oxford, ENGLAND
Available from: 2018-03-26 Created: 2018-03-26 Last updated: 2018-03-26Bibliographically approved
Hantke, M. F., Hasse, D., Ekeberg, T., John, K., Svenda, M., Loh, D., . . . Maia, F. R. .. (2016). A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3, Article ID 160061.
Open this publication in new window or tab >>A data set from flash X-ray imaging of carboxysomes
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed) Published
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.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300202 (URN)10.1038/sdata.2016.61 (DOI)000390225400006 ()
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
van der Schot, G., Svenda, M., Maia, F. R. .., Hantke, M. F., DePonte, D. P., Seibert, M. M., . . . Ekeberg, T. (2016). Open data set of live cyanobacterial cells imaged using an X-ray laser. Scientific Data, 3, Article ID 160058.
Open this publication in new window or tab >>Open data set of live cyanobacterial cells imaged using an X-ray laser
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160058Article in journal (Refereed) Published
Abstract [en]

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300201 (URN)10.1038/sdata.2016.58 (DOI)000390225400003 ()
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
Ekeberg, T., Svenda, M., Seibert, M. M., Abergel, C., Maia, F. R. .., Seltzer, V., . . . Hajdu, J. (2016). Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. Scientific Data, 3, Article ID UNSP 160060.
Open this publication in new window or tab >>Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160060Article in journal (Refereed) Published
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.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-314814 (URN)10.1038/sdata.2016.60 (DOI)000390225400005 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilStiftelsen Olle Engkvist Byggmästare
Available from: 2017-02-07 Created: 2017-02-06 Last updated: 2017-11-29Bibliographically approved
van der Schot, G., Svenda, M., Maia, F. R. N., Hantke, M., DePonte, D. P., Seibert, M. M., . . . Ekeberg, T. (2015). Imaging single cells in a beam of live cyanobacteria with an X-ray laser. Nature Communications, 6, Article ID 5704.
Open this publication in new window or tab >>Imaging single cells in a beam of live cyanobacteria with an X-ray laser
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2015 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 5704Article in journal (Refereed) Published
Abstract [en]

There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-245040 (URN)10.1038/ncomms6704 (DOI)000350034400002 ()25669616 (PubMedID)
Available from: 2015-02-24 Created: 2015-02-24 Last updated: 2017-12-04Bibliographically approved
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