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,Tara Michels-Clark,William I Weis,Minglei Zhao,Nicholas K Sauter,James M Holton,Oliver B Zeldin,Aaron S Brewster,Qiangjun Zhou,Monarin Uervirojnangkoorn,Axel T Brunger

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.

Highlights

X-ray free electron laser (XFEL) crystallography is an emerging technique for obtaining high-resolution diffraction data from macromolecular crystals (Schlichting, 2015)
Advances to our XFEL diffraction data processing system resulted in somewhat better statistics of a diffraction data set and refined atomic model for the crystal structure of the Syt1–SNARE complex than that previously reported (Zhou et al, 2015)
Compared with a lower resolution synchrotron diffraction data set obtained from similar crystals in the same crystal form, the electron density maps calculated from the XFEL data contained more information, especially for many side chains

Summary

Introduction

X-ray free electron laser (XFEL) crystallography is an emerging technique for obtaining high-resolution diffraction data from macromolecular crystals (Schlichting, 2015). Diffraction data from an XFEL pulse lasting only tens of femtoseconds are largely free from X-ray induced radiation damage that might otherwise affect the success of crystallographic phasing and atomic model refinement. The crystal is effectively stationary during the XFEL pulse, which complicates determination of the crystal lattice model from the resulting zero-rotation or ’still’ diffraction images. The XFEL pulse destroys or damages the illuminated crystal volume and allows only a single diffraction image to be collected. This effect is exacerbated by the variation in intensity and spectrum

Methods

Results

Conclusion