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

Abstract
Data availability
Article and author information
Metrics

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.

Data availability

The following data sets were generated

1. Lyubimov AY
2. Uervirojnangkoorn M
3. Zhou Q
4. Zhao M
5. Sauter NK
6. Brewster AS
7. Weis WI
8. Brunger AT
(2016) Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction
Publicly available at the RCSB Protein Data Bank (accession no: 5KJ7).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5KJ7
1. Lyubimov AY
2. Uervirojnangkoorn M
3. Zhou Q
4. Zhao M
5. Sauter NK
6. Brewster AS
7. Weis WI
8. Brunger AT
(2016) Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction
Publicly available at the RCSB Protein Data Bank (accession no: 5KJ8).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5KJ8

Article and author information

Author details

Artem Y Lyubimov

Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States

Competing interests
No competing interests declared.
Monarin Uervirojnangkoorn

Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States

Competing interests
No competing interests declared.
Oliver B Zeldin

Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States

Competing interests
No competing interests declared.
Qiangjun Zhou

Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States

Competing interests
No competing interests declared.
Minglei Zhao

Department of Molecular and Cellular Physiology, Stanford University Medical Center, Stanford, United States

Competing interests
No competing interests declared.
Aaron S Brewster

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States

Competing interests
No competing interests declared.
Tara Michels-Clark

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States

Competing interests
No competing interests declared.
James M Holton

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States

Competing interests
No competing interests declared.
Nicholas K Sauter

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States

Competing interests
No competing interests declared.
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.
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.

"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.

Copyright

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.