1. Structural Biology and Molecular Biophysics
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Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex

  1. Artem Y Lyubimov
  2. Monarin Uervirojnangkoorn
  3. Oliver B Zeldin
  4. Qiangjun Zhou
  5. Minglei Zhao
  6. Aaron S Brewster
  7. Tara Michels-Clark
  8. James M Holton
  9. Nicholas K Sauter
  10. William I Weis  Is a corresponding author
  11. Axel T Brunger  Is a corresponding author
  1. Stanford University Medical Center, United States
  2. Lawrence Berkeley National Laboratory, United States
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Cite this article as: eLife 2016;5:e18740 doi: 10.7554/eLife.18740

Abstract

X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models.

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The following data sets were generated

Article and author information

Author details

  1. Artem Y Lyubimov

    Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States
    Competing interests
    No competing interests declared.
  2. Monarin Uervirojnangkoorn

    Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States
    Competing interests
    No competing interests declared.
  3. Oliver B Zeldin

    Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States
    Competing interests
    No competing interests declared.
  4. Qiangjun Zhou

    Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States
    Competing interests
    No competing interests declared.
  5. Minglei Zhao

    Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States
    Competing interests
    No competing interests declared.
  6. Aaron S Brewster

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.
  7. Tara Michels-Clark

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.
  8. James M Holton

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.
  9. Nicholas K Sauter

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.
  10. William I Weis

    Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States
    For correspondence
    weis@stanford.edu
    Competing interests
    William I Weis, Reviewing editor for eLife.
  11. Axel T Brunger

    Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States
    For correspondence
    brunger@stanford.edu
    Competing interests
    Axel T Brunger, Reviewing editor for eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5121-2036

Funding

Howard Hughes Medical Institute (Collaborative Innovation Award)

  • William I Weis
  • Axel T Brunger

National Institutes of Health (R01GM102520)

  • Nicholas K Sauter

National Institutes of Health (R01GM117126)

  • Nicholas K Sauter

National Institute of General Medical Sciences (P41 GM103403)

  • Axel T Brunger

National Institutes of Health (S10 RR029205)

  • Axel T Brunger

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Stephen C. Harrison, Harvard Medical School, United States

Publication history

  1. Received: June 12, 2016
  2. Accepted: October 11, 2016
  3. Accepted Manuscript published: October 12, 2016 (version 1)
  4. Version of Record published: November 3, 2016 (version 2)

Copyright

© 2016, Lyubimov et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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