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Title: Improving signal strength in serial crystallography with DIALS geometry refinement

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 reducesmore » 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.« less
Authors:
 [1] ; ORCiD logo [2] ;  [3] ;  [4] ; ORCiD logo [1] ; ORCiD logo [1] ;  [1] ;  [4] ; ORCiD logo [4] ;  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Science and Technology Facilities Council (STFC), Oxford (United Kingdom). Rutherford Appleton Lab. (RAL)
  3. Science and Technology Facilities Council (STFC), Harwell Campus, Oxford (United Kingdom). Diamond Light Source, Ltd.; MRC Lab. of Molecular Biology (United Kingdom)
  4. Science and Technology Facilities Council (STFC), Harwell Campus, Oxford (United Kingdom). Diamond Light Source, Ltd.
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 74; Journal Issue: 9; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE
OSTI Identifier:
1468376
Alternate Identifier(s):
OSTI ID: 1477374

Brewster, Aaron S., Waterman, David G., Parkhurst, James M., Gildea, Richard J., Young, Iris D., O'Riordan, Lee J., Yano, Junko, Winter, Graeme, Evans, Gwyndaf, and Sauter, Nicholas K.. Improving signal strength in serial crystallography with DIALS geometry refinement. United States: N. p., Web. doi:10.1107/S2059798318009191.
Brewster, Aaron S., Waterman, David G., Parkhurst, James M., Gildea, Richard J., Young, Iris D., O'Riordan, Lee J., Yano, Junko, Winter, Graeme, Evans, Gwyndaf, & Sauter, Nicholas K.. Improving signal strength in serial crystallography with DIALS geometry refinement. United States. doi:10.1107/S2059798318009191.
Brewster, Aaron S., Waterman, David G., Parkhurst, James M., Gildea, Richard J., Young, Iris D., O'Riordan, Lee J., Yano, Junko, Winter, Graeme, Evans, Gwyndaf, and Sauter, Nicholas K.. 2018. "Improving signal strength in serial crystallography with DIALS geometry refinement". United States. doi:10.1107/S2059798318009191.
@article{osti_1468376,
title = {Improving signal strength in serial crystallography with DIALS geometry refinement},
author = {Brewster, Aaron S. and Waterman, David G. and Parkhurst, James M. and Gildea, Richard J. and Young, Iris D. and O'Riordan, Lee J. and Yano, Junko and Winter, Graeme and Evans, Gwyndaf and Sauter, Nicholas K.},
abstractNote = {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.},
doi = {10.1107/S2059798318009191},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 9,
volume = 74,
place = {United States},
year = {2018},
month = {9}
}

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Scaling and assessment of data quality
journal, December 2005
  • Evans, Philip
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Nanoflow electrospinning serial femtosecond crystallography
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