Abstract
The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied. Since the optimal models for metrology and crystal orientation are interdependent, alternate cycles of panel refinement and crystal refinement have been required. To simplify the process, a sparse linear algebra technique for solving the normal equations was implemented, allowing the detector panels to be refined simultaneously against the diffraction from thousands of crystals with excellent computational performance. Separately, it is shown how to refine the metrology of a second CSPAD detector, positioned at a distance of 2.5 m from the crystal, used for recording low-angle reflections. With the ability to jointly refine the detector position against the ensemble of all crystals used for structure determination, it is shown that ensemble refinement greatly reduces the apparent nonisomorphism that is often observed in the unit-cell distributions from still-shot serial crystallography. In addition, it is shown that batching the images by timestamp and re-refining the detector position can realistically model small, time-dependent variations in detector position relative to the sample, and thereby improve the integrated structure-factor intensity signal and heavy-atom anomalous peak heights.
Highlights
Serial crystallographic methods are widening the scope of structural biology, allowing the examination of macromolecular structure with short radiation pulses that generate diffraction from samples nearly free of radiation damage
We show below how the DIALS framework can be adapted to describe serial crystallography experiments involving two imaging detectors at different crystal-to-detector distances (x5) and how the simultaneous refinement of detector and crystal models improves the accuracy of poorly measured unit-cell axis lengths for unit-cell axes that are oriented nearly parallel to the X-ray beam (x6)
We refined the CSPAD detector metrology using customwritten code for serial crystallography incorporated into dials.refine. x3.1 describes the hierarchical organization of the CSPAD and x3.2 describes the automatic determination of initial quadrant locations using powder patterns
Summary
Serial crystallographic methods are widening the scope of structural biology, allowing the examination of macromolecular structure with short radiation pulses that generate diffraction from samples nearly free of radiation damage. A better software design, adopted here, is to maintain two data structures, one that contains the original detector-panel measurements in their unaltered forms (as a list of rectangular sensor arrays of pixels) and another that represents the complete vector description of each panel, including the origin vector d0 that locates the panel in relation to the crystal and two vectors dx and dy that define the fast and slow readout directions (Parkhurst et al, 2014) This approach removes the undesirable requirements in Ha14 that all detector panels are coplanar and that the plane of the detector is normal to the beam. Considering recent reports from other groups describing how small changes in the crystal-to-detector distance can affect experimental results (Nass et al, 2016), we develop a procedure to discover small time-dependent changes in the distance, thereby improving the integrated Bragg spot signal (x7)
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