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Improving signal strength in serial crystallography with DIALS geometry refinement

DOI: 10.1107/S2059798318009191 DOI Help

Authors: Aaron S. Brewster (Lawrence Berkeley National Laboratory) , David G. Waterman (STFC Rutherford Appleton Laboratory; CCP4) , James Parkhurst (Diamond Light Source; MRC Laboratory of Molecular Biology) , Richard J. Gildea (Diamond Light Source) , Iris D. Young (Lawrence Berkeley National Laboratory) , Lee J. O'Riordan (Lawrence Berkeley National Laboratory) , Junko Yano (Lawrence Berkeley National Laboratory) , Graeme Winter (Diamond Light Source) , Gwyndaf Evans (Diamond Light Source) , Nicholas K. Sauter (Lawrence Berkeley National Laboratory)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Acta Crystallographica Section D Structural Biology , VOL 74 , PAGES 877 - 894

State: Published (Approved)
Published: September 2018

Open Access Open Access

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.

Journal Keywords: XFEL; metrology; DIALS; refinement; sparse algebra

Subject Areas: Information and Communication Technology, Biology and Bio-materials

Facility: LCLS

Added On: 10/09/2018 11:21

Discipline Tags:

Computing & software technologies Information & Communication Technologies Structural biology Data processing Life Sciences & Biotech

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