Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns.

Monarin Uervirojnangkoorn,William I Weis,Axel T Brunger,Artem Y Lyubimov,Qiangjun Zhou

doi:10.1107/s2059798318013177

Abstract

Processing X-ray free-electron laser (XFEL) diffraction images poses challenges, as an XFEL pulse is powerful enough to destroy or damage the diffracting volume and thereby yields only one diffraction image per volume. Moreover, the crystal is stationary during the femtosecond pulse, so reflections are generally only partially recorded. Therefore, each XFEL diffraction image must be scaled individually and, ideally, corrected for partiality prior to merging. An additional complication may arise owing to indexing ambiguities when the symmetry of the Bravais lattice is higher than that of the space group, or when the unit-cell dimensions are similar to each other. Here, an automated method is presented that diagnoses these indexing ambiguities based on the Brehm-Diederichs algorithm [Brehm & Diederichs (2014), Acta Cryst. D70, 101-109] and produces a consistent indexing choice for the large majority of diffraction images. This method was applied to an XFEL diffraction data set measured from crystals of the neuronal SNARE-complexin-1-synaptotagmin-1 complex. After correcting the indexing ambiguities, substantial improvements were observed in the merging statistics and the atomic model refinement R values. This method should be a useful addition to the arsenal of tools for the processing of XFEL diffraction data sets.

Highlights

An X-ray free-electron laser (XFEL) pulse generated by the Linac Coherent Light Source (LCLS) typically delivers $1011 photons in $40 fs
An XFEL pulse generated by the Linac Coherent Light Source (LCLS) typically delivers $1011 photons in $40 fs
We applied this method to process XFEL diffraction images obtained from crystals of the neuronal SNARE–complexin-1– synaptotagmin-1 complex (Zhou et al, 2017) in order to resolve the indexing ambiguity that arose from two similar unit-cell dimensions in space group P21212

Summary

Introduction

An XFEL pulse generated by the Linac Coherent Light Source (LCLS) typically delivers $1011 photons in $40 fs. For typical macromolecular crystal mosaicities and X-ray energy bandpasses, all recorded XFEL reflection intensities are partial Each of these still images has to be individually indexed in order to obtain the crystal orientation and unit-cell dimensions, and individually scaled, integrated, corrected for partiality and merged in order to obtain a complete diffraction data set. We implemented a bootstrap procedure that uses only a subset of the diffraction images to calculate the correlation matrix used in the Brehm–Diederichs algorithm We applied this method to process XFEL diffraction images obtained from crystals of the neuronal SNARE–complexin-1– synaptotagmin-1 complex (Zhou et al, 2017) in order to resolve the indexing ambiguity that arose from two similar unit-cell dimensions in space group P21212. This result illustrates the efficiency of our method, which can be used even in the case of large XFEL diffraction data sets obtained using liquid jet sample delivery techniques

XFEL diffraction data collection

Indexing and integration of the XFEL diffraction images

Resolving the indexing ambiguity of the XFEL diffraction data

Synchrotron data collection and processing

Results and discussion