1. Structural Biology and Molecular Biophysics

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

  1. Monarin Uervirojnangkoorn
  2. Oliver B Zeldin
  3. Artem Y Lyubimov
  4. Johan Hattne
  5. Aaron S Brewster
  6. Nicholas K Sauter
  7. Axel T Brunger
  8. William I Weis  Is a corresponding author
  1. Howard Hughes Medical Institute, Stanford University, United States
  2. Janelia Research Campus, United States
  3. Lawrence Berkeley National Laboratory, United States
  4. Stanford University, United States
https://doi.org/10.7554/eLife.05421
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  1. Monarin Uervirojnangkoorn
  2. Oliver B Zeldin
  3. Artem Y Lyubimov
  4. Johan Hattne
  5. Aaron S Brewster
  6. Nicholas K Sauter
  7. Axel T Brunger
  8. William I Weis
(2015)
Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
eLife 4:e05421.
https://doi.org/10.7554/eLife.05421
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Abstract

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

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Author details

  1. Monarin Uervirojnangkoorn

    Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  2. Oliver B Zeldin

    Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  3. Artem Y Lyubimov

    Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  4. Johan Hattne

    Janelia Research Campus, Ashburn, United States
    Competing interests
    No competing interests declared.

  5. Aaron S Brewster

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.

  6. Nicholas K Sauter

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    No competing interests declared.

  7. Axel T Brunger

    Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
    Competing interests
    Axel T Brunger, Reviewing editor, eLife.

  8. William I Weis

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
    For correspondence
    bill.weis@stanford.edu
    Competing interests
    No competing interests declared.

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This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Monarin Uervirojnangkoorn
  2. Oliver B Zeldin
  3. Artem Y Lyubimov
  4. Johan Hattne
  5. Aaron S Brewster
  6. Nicholas K Sauter
  7. Axel T Brunger
  8. William I Weis
(2015)
Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
eLife 4:e05421.
https://doi.org/10.7554/eLife.05421

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https://doi.org/10.7554/eLife.05421

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Further reading

    1. Structural Biology and Molecular Biophysics

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

    Artem Y Lyubimov, Monarin Uervirojnangkoorn ... Axel T Brunger
    Research Advance Updated

    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.