Breaking the indexing ambiguity in serial crystallography

Abstract

In serial crystallography, a very incomplete partial data set is obtained from each diffraction experiment (a `snapshot'). In some space groups, an indexing ambiguity exists which requires that the indexing mode of each snapshot needs to be established with respect to a reference data set. In the absence of such re‐indexing information, crystallographers have thus far resorted to a straight merging of all snapshots, yielding a perfectly twinned data set of higher symmetry which is poorly suited for structure solution and refinement. Here, two algorithms have been designed for assembling complete data sets by clustering those snapshots that are indexed in the same way, and they have been tested using 15 445 snapshots from photosystem I [Chapman et al. (2011), Nature (London), 470, 73–77] and with noisy model data. The results of the clustering are unambiguous and enabled the construction of complete data sets in the correct space group P63 instead of (twinned) P6322 that researchers have been forced to use previously in such cases of indexing ambiguity. The algorithms thus extend the applicability and reach of serial crystallography.

New methods for indexing multi-lattice diffraction data

“…Regardless of the fact that still shots from two randomly oriented crystals will share only a few common Miller indices, the correlation coefficient between those shared structurefactor intensities will be highest if the two images have been indexed with the same sense. An implementation of algorithm 2 of Brehm & Diederichs (2014) was developed in the context of cctbx.xfel , and in x4.2 we demonstrate the application of the algorithm to synchrotron data in space group I23. Table 1 Data-reduction statistics for the semi-synthetic multi-lattice data sets, including overlapping reflections.…”

“…The space group I23 can be indexed in one of two ways; hence, it was necessary to ensure that all lattices were indexed in a consistent manner. This was achieved using the algorithm of Brehm & Diederichs (2014) as described in x3.8, which showed a clear separation of the two indexing modes (Fig. 11). 4.3.…”

“…If available, a more complete but lowresolution data set may be used as a reference, or calculated structure factors may be used if the structure is already known. Brehm & Diederichs (2014) introduced an elegant way of breaking the indexing ambiguity in XFEL data sets, which may comprise many thousands to hundreds of thousands of very incomplete partial data sets taken from still shots. The approach rests upon a comparison of pairs of images.…”

Direct Phasing of Finite Crystals Illuminated with a Free-Electron Laser

“…Our auto-indexing routine was not vulnerable to indexing ambiguities because we knew a priori the approximate orientation of each target-we would have otherwise needed to include the peak intensity information in the reciprocal-lattice determination [44].…”

Solvent minimization induces preferential orientation and crystal clustering in serial micro-crystallography on micro-meshes,in situplates and on a movable crystal conveyor belt

“…Dealing with single 6 rotations was slightly more problematic (uncertainty in the crystal mosaicity impeded merging images that only shared a handful of simultaneously recorded reflections, so the 'keystone' images were more difficult to assemble). A more robust strategy for merging data in polar space groups was recently described (Brehm & Diederichs, 2014).…”