Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex
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 numbe...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2016-10-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/18740 |
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doaj-e9788a81936e49069eb9cafbcab50732 |
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Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Artem Y Lyubimov Monarin Uervirojnangkoorn Oliver B Zeldin Qiangjun Zhou Minglei Zhao Aaron S Brewster Tara Michels-Clark James M Holton Nicholas K Sauter William I Weis Axel T Brunger |
| spellingShingle |
Artem Y Lyubimov Monarin Uervirojnangkoorn Oliver B Zeldin Qiangjun Zhou Minglei Zhao Aaron S Brewster Tara Michels-Clark James M Holton Nicholas K Sauter William I Weis Axel T Brunger Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex eLife macromolecular crystallography X-ray free electron laser radiation damage post-refinement |
| author_facet |
Artem Y Lyubimov Monarin Uervirojnangkoorn Oliver B Zeldin Qiangjun Zhou Minglei Zhao Aaron S Brewster Tara Michels-Clark James M Holton Nicholas K Sauter William I Weis Axel T Brunger |
| author_sort |
Artem Y Lyubimov |
| title |
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex |
| title_short |
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex |
| title_full |
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex |
| title_fullStr |
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex |
| title_full_unstemmed |
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex |
| title_sort |
advances in x-ray free electron laser (xfel) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / snare complex |
| publisher |
eLife Sciences Publications Ltd |
| series |
eLife |
| issn |
2050-084X |
| publishDate |
2016-10-01 |
| description |
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. |
| topic |
macromolecular crystallography X-ray free electron laser radiation damage post-refinement |
| url |
https://elifesciences.org/articles/18740 |
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doaj-e9788a81936e49069eb9cafbcab507322021-05-05T00:38:13ZengeLife Sciences Publications LtdeLife2050-084X2016-10-01510.7554/eLife.18740Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complexArtem Y Lyubimov0Monarin Uervirojnangkoorn1Oliver B Zeldin2Qiangjun Zhou3Minglei Zhao4Aaron S Brewster5Tara Michels-Clark6James M Holton7Nicholas K Sauter8William I Weis9Axel T Brunger10https://orcid.org/0000-0001-5121-2036Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Neurology and Neurological Science, Stanford University, Stanford, United States; Structural Biology, Stanford University, Stanford, United States; Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United StatesDepartment of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Neurology and Neurological Science, Stanford University, Stanford, United States; Photon Science, Stanford University, Stanford, United States; Structural Biology, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United StatesDepartment of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Neurology and Neurological Science, Stanford University, Stanford, United States; Photon Science, Stanford University, Stanford, United States; Structural Biology, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United StatesDepartment of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Neurology and Neurological Science, Stanford University, Stanford, United States; Photon Science, Stanford University, Stanford, United States; Structural Biology, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United StatesDepartment of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Neurology and Neurological Science, Stanford University, Stanford, United States; Photon Science, Stanford University, Stanford, United States; Structural Biology, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United StatesMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United StatesMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United StatesMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United StatesMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United StatesDepartment of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Structural Biology, Stanford University, Stanford, United States; Photon Science, Stanford University, Stanford, United StatesDepartment of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Neurology and Neurological Science, Stanford University, Stanford, United States; Photon Science, Stanford University, Stanford, United States; Structural Biology, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United StatesX-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.https://elifesciences.org/articles/18740macromolecular crystallographyX-ray free electron laserradiation damagepost-refinement |