Abstract
SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008 ▸), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012 ▸), J. Appl. Cryst. 45, 335-341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
Highlights
The high brightness and femtosecond pulse duration of X-ray free-electron lasers (XFELs) enabled the serial diffractionbefore-destruction paradigm (Neutze et al, 2000), which mitigates X-ray radiation damage and allows data to be collected from weakly scattering targets
Femtosecond XFEL pulses are too short for substantial crystal rotation during exposure, so only partial reflection intensities are recorded in each diffraction pattern, with partiality determined by various factors such as X-ray bandwidth and crystal shape, size, orientation and mosaicity
In order to test the ability of SPIND to index sparse diffraction patterns, we simulated 400 diffraction patterns from 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) crystals (Beck & Sheldrick, 2008) at random orientations
Summary
The high brightness and femtosecond pulse duration of X-ray free-electron lasers (XFELs) enabled the serial diffractionbefore-destruction paradigm (Neutze et al, 2000), which mitigates X-ray radiation damage and allows data to be collected from weakly scattering targets. In a typical serial femtosecond crystallography (SFX) experiment, diffraction patterns are recorded from tens of thousands of microcrystals delivered sequentially across a pulsed X-ray beam [Chapman et al (2011); see Spence (2017) for a review]. These snapshot diffraction patterns (from individual microcrystals) correspond to reciprocal-space intensity samples that lie on the surface of the Ewald sphere. Femtosecond XFEL pulses are too short for substantial crystal rotation during exposure, so only partial reflection intensities are recorded in each diffraction pattern, with partiality determined by various factors such as X-ray bandwidth and crystal shape, size, orientation and mosaicity.
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