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Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free- Electron Laser Science, Deutsches Elektronen-Synchrotron.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Czech Academy of Science, Chalmers University of Technology.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
2017 (English)In: IUCrJ, Vol. 4, no 6Article in journal (Refereed) Published
Abstract [en]

Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

Place, publisher, year, edition, pages
2017. Vol. 4, no 6
Keyword [en]
hit detection, plasma emission spectra, serial femtosecond crystallography, protein structure
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-331934DOI: 10.1107/S2052252517014154OAI: oai:DiVA.org:uu-331934DiVA: diva2:1152589
Available from: 2017-10-25 Created: 2017-10-25 Last updated: 2017-10-25
In thesis
1. Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
Open this publication in new window or tab >>Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins.                   

We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography.

The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution.

Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal.

The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. 78 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1592
Keyword
X-ray free-electron laser; Serial Femtosecond Crystallography; Radiation Damage; Plasma Simulations; Ultrafast Lasers; X-ray Imaging; Diffraction Theory; Ultrafast Phenomena; Hit Detection; Plasma Emission Spectra; Serial Femtosecond Crystallography; Protein Structure; Protein Crystallography; Metalloprotein; Non-thermal Heating; Water; Ferredoxin; NLTE Simulation; XFEL; FEL; SFX
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-331936 (URN)978-91-513-0134-1 (ISBN)
Public defence
2017-12-15, Polhemssalen, Lägerhyddsvägen 1, Uppsala, 09:15 (English)
Opponent
Supervisors
Funder
Swedish Foundation for Strategic Research , ICA10-0090Swedish Research Council, 2013-3940The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2017-11-22 Created: 2017-10-25 Last updated: 2017-11-22

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