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Title: Analysis of XFEL serial diffraction data from individual crystalline fibrils

Abstract

Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. In conclusion, the advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.

Authors:
 [1];  [2];  [3];  [4];  [5];  [2];  [2];  [6];  [2];  [2];  [2];  [7];  [2];  [2];  [2];  [8];  [2];  [9];  [10];  [11] more »;  [3];  [2];  [2];  [8];  [3];  [3];  [2];  [4];  [12];  [1] « less
  1. Univ. of Canterbury, Christchurch (New Zealand)
  2. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  4. Institut Laue-Langevin, Grenoble (France); Keele Univ. (England)
  5. European Synchrotron Radiation Facility, Grenoble (France)
  6. European XFEL GmbH, Hamburg (Germany)
  7. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Max Planck Institute of Biochemistry, Martinsried (Germany)
  8. Univ. of Crete and IESL/FORTH, Crete (Greece)
  9. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Max-Planck Institute for the Structure and Dynamics of Matter, Hamburg (Germany)
  10. Univ. Grenoble Alpes, Grenoble (France)
  11. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  12. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1416058
Grant/Contract Number:
AC52-07NA27344; 1R01GM117342-01; AC02- 76SF00515
Resource Type:
Journal Article: Published Article
Journal Name:
IUCrJ
Additional Journal Information:
Journal Volume: 4; Journal Issue: 6; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; serial crystallography; coherent X-ray diffractive imaging (CXDI); single particles; molecular orientation determination; crystalline fibrils; amyloid

Citation Formats

Wojtas, David H., Ayyer, Kartik, Liang, Mengning, Mossou, Estelle, Romoli, Filippo, Seuring, Carolin, Beyerlein, Kenneth R., Bean, Richard J., Morgan, Andrew J., Oberthuer, Dominik, Fleckenstein, Holger, Heymann, Michael, Gati, Cornelius, Yefanov, Oleksandr, Barthelmess, Miriam, Ornithopoulou, Eirini, Galli, Lorenzo, Xavier, P. Lourdu, Ling, Wai Li, Frank, Matthias, Yoon, Chun Hong, White, Thomas A., Bajt, Saša, Mitraki, Anna, Boutet, Sebastien, Aquila, Andrew, Barty, Anton, Forsyth, V. Trevor, Chapman, Henry N., and Millane, Rick P. Analysis of XFEL serial diffraction data from individual crystalline fibrils. United States: N. p., 2017. Web. doi:10.1107/S2052252517014324.
Wojtas, David H., Ayyer, Kartik, Liang, Mengning, Mossou, Estelle, Romoli, Filippo, Seuring, Carolin, Beyerlein, Kenneth R., Bean, Richard J., Morgan, Andrew J., Oberthuer, Dominik, Fleckenstein, Holger, Heymann, Michael, Gati, Cornelius, Yefanov, Oleksandr, Barthelmess, Miriam, Ornithopoulou, Eirini, Galli, Lorenzo, Xavier, P. Lourdu, Ling, Wai Li, Frank, Matthias, Yoon, Chun Hong, White, Thomas A., Bajt, Saša, Mitraki, Anna, Boutet, Sebastien, Aquila, Andrew, Barty, Anton, Forsyth, V. Trevor, Chapman, Henry N., & Millane, Rick P. Analysis of XFEL serial diffraction data from individual crystalline fibrils. United States. doi:10.1107/S2052252517014324.
Wojtas, David H., Ayyer, Kartik, Liang, Mengning, Mossou, Estelle, Romoli, Filippo, Seuring, Carolin, Beyerlein, Kenneth R., Bean, Richard J., Morgan, Andrew J., Oberthuer, Dominik, Fleckenstein, Holger, Heymann, Michael, Gati, Cornelius, Yefanov, Oleksandr, Barthelmess, Miriam, Ornithopoulou, Eirini, Galli, Lorenzo, Xavier, P. Lourdu, Ling, Wai Li, Frank, Matthias, Yoon, Chun Hong, White, Thomas A., Bajt, Saša, Mitraki, Anna, Boutet, Sebastien, Aquila, Andrew, Barty, Anton, Forsyth, V. Trevor, Chapman, Henry N., and Millane, Rick P. 2017. "Analysis of XFEL serial diffraction data from individual crystalline fibrils". United States. doi:10.1107/S2052252517014324.
@article{osti_1416058,
title = {Analysis of XFEL serial diffraction data from individual crystalline fibrils},
author = {Wojtas, David H. and Ayyer, Kartik and Liang, Mengning and Mossou, Estelle and Romoli, Filippo and Seuring, Carolin and Beyerlein, Kenneth R. and Bean, Richard J. and Morgan, Andrew J. and Oberthuer, Dominik and Fleckenstein, Holger and Heymann, Michael and Gati, Cornelius and Yefanov, Oleksandr and Barthelmess, Miriam and Ornithopoulou, Eirini and Galli, Lorenzo and Xavier, P. Lourdu and Ling, Wai Li and Frank, Matthias and Yoon, Chun Hong and White, Thomas A. and Bajt, Saša and Mitraki, Anna and Boutet, Sebastien and Aquila, Andrew and Barty, Anton and Forsyth, V. Trevor and Chapman, Henry N. and Millane, Rick P.},
abstractNote = {Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. In conclusion, the advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.},
doi = {10.1107/S2052252517014324},
journal = {IUCrJ},
number = 6,
volume = 4,
place = {United States},
year = 2017,
month =
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1107/S2052252517014324

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  • Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. In conclusion, the advantages of this technique should allowmore » structural studies of fibrous systems in biology that are inaccessible using existing techniques.« less
  • X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core–shell architecture were used as a model system for proof-of-principle coherentmore » diffractive single-particle imaging experiments. To deal with the heterogeneity of the core–shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core–shell architecture.« less
  • Serial crystallography, using either femtosecond X-ray pulses from free-electron laser sources or short synchrotron-radiation exposures, has the potential to reveal metalloprotein structural details while minimizing damage processes. However, deriving a self-consistent set of Bragg intensities from numerous still-crystal exposures remains a difficult problem, with optimal protocols likely to be quite different from those well established for rotation photography. Here several data processing issues unique to serial crystallography are examined. It is found that the limiting resolution differs for each shot, an effect that is likely to be due to both the sample heterogeneity and pulse-to-pulse variation in experimental conditions. Shotsmore » with lower resolution limits produce lower-quality models for predicting Bragg spot positions during the integration step. Also, still shots by their nature record only partial measurements of the Bragg intensity. An approximate model that corrects to the full-spot equivalent (with the simplifying assumption that the X-rays are monochromatic) brings the distribution of intensities closer to that expected from an ideal crystal, and improves the sharpness of anomalous difference Fourier peaks indicating metal positions.« less
  • Serial crystallography, using either femtosecond X-ray pulses from free-electron laser sources or short synchrotron-radiation exposures, has the potential to reveal metalloprotein structural details while minimizing damage processes. However, deriving a self-consistent set of Bragg intensities from numerous still-crystal exposures remains a difficult problem, with optimal protocols likely to be quite different from those well established for rotation photography. Here several data processing issues unique to serial crystallography are examined. It is found that the limiting resolution differs for each shot, an effect that is likely to be due to both the sample heterogeneity and pulse-to-pulse variation in experimental conditions. Shotsmore » with lower resolution limits produce lower-quality models for predicting Bragg spot positions during the integration step. Also, still shots by their nature record only partial measurements of the Bragg intensity. An approximate model that corrects to the full-spot equivalent (with the simplifying assumption that the X-rays are monochromatic) brings the distribution of intensities closer to that expected from an ideal crystal, and improves the sharpness of anomalous difference Fourier peaks indicating metal positions.« less