Gold Standard for macromolecular crystallography diffraction data

Bernstein, H; Förster, A.; Bhowmick, A.; Brewster, A.; Brockhauser, S.; Gelisio, L.; Hall, D.; Leonarski, F.; Mariani, V.; Santoni, G.; Vonrhein, C.; Winter, G.

doi:10.1107/S2052252520008672

Gold Standard for macromolecular crystallography diffraction data

Journal Article · 01 January 2022 · IUCrJ

DOI:https://doi.org/10.1107/S2052252520008672· OSTI ID:1690168

Bernstein, H; Förster, A.; Bhowmick, A.; Brewster, A.; Brockhauser, S.; Gelisio, L.; Hall, D.; Leonarski, F.; Mariani, V.; Santoni, G.; Vonrhein, C.; Winter, G.

Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: ~OTHER

DOE Contract Number:: SC0012704

OSTI ID:: 1690168

Report Number(s):: BNL-220490-2020-JACI

Journal Information:: IUCrJ, Vol. 7, Issue 5

Country of Publication:: United States

Language:: English

References (30)

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB) Adams, Paul D.; Afonine, Pavel V.; Baskaran, Kumaran Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 4 https://doi.org/10.1107/S2059798319004522	journal	April 2019
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910048675	journal	March 2011
The protein data bank: A computer-based archival file for macromolecular structures Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B. Journal of Molecular Biology, Vol. 112, Issue 3 https://doi.org/10.1016/S0022-2836(77)80200-3	journal	May 1977
What every experimentalist needs to know about recording essential metadata of primary ( i.e. raw) diffraction data Bernstein, Herbert J. Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a1 https://doi.org/10.1107/S0108767317098130	journal	December 2017
Best practices for high data-rate macromolecular crystallography (HDRMX) Bernstein, Herbert J.; Andrews, Lawrence C.; Diaz, Jorge A. Structural Dynamics, Vol. 7, Issue 1 https://doi.org/10.1063/1.5128498	journal	January 2020
Meeting Report: Workshop on Beamline Integration and Data Formatting Donath, Tilman; Rissi, Michael; Billich, Heiner Synchrotron Radiation News, Vol. 26, Issue 5 https://doi.org/10.1080/08940886.2013.832589	journal	September 2013
The crystallographic information file (CIF): a new standard archive file for crystallography Hall, S. R.; Allen, F. H.; Brown, I. D. Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 6 https://doi.org/10.1107/S010876739101067X	journal	November 1991
The Karabo distributed control system Hauf, Steffen; Heisen, Burkhard; Aplin, Steve Journal of Synchrotron Radiation, Vol. 26, Issue 5 https://doi.org/10.1107/S1600577519006696	journal	August 2019
FACT and FAIR with Big Data allows objectivity in science: The view of crystallography Helliwell, John R. Structural Dynamics, Vol. 6, Issue 5 https://doi.org/10.1063/1.5124439	journal	September 2019
A new golden age for computer architecture Hennessy, John L.; Patterson, David A. Communications of the ACM, Vol. 62, Issue 2 https://doi.org/10.1145/3282307	journal	January 2019
A Robust, Format-Agnostic Scientific Data Transfer Framework Hester, James Data Science Journal, Vol. 15, Issue 0 https://doi.org/10.5334/dsj-2016-012	journal	January 2016
Experimental station Bernina at SwissFEL: condensed matter physics on femtosecond time scales investigated by X-ray diffraction and spectroscopic methods Ingold, Gerhard; Abela, Rafael; Arrell, Christopher Journal of Synchrotron Radiation, Vol. 26, Issue 3 https://doi.org/10.1107/S160057751900331X	journal	April 2019
Deposition of structure factors at the Protein Data Bank Jiang, Jiansheng; Abola, Enrique; Sussman, Joel L. Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 1 https://doi.org/10.1107/S0907444998016631	journal	January 1999
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
The NeXus data format Könnecke, Mark; Akeroyd, Frederick A.; Bernstein, Herbert J. Journal of Applied Crystallography, Vol. 48, Issue 1 https://doi.org/10.1107/S1600576714027575	journal	January 2015
Characterization and Calibration of PILATUS Detectors Kraft, P.; Bergamaschi, A.; Bronnimann, Ch. IEEE Transactions on Nuclear Science, Vol. 56, Issue 3 https://doi.org/10.1109/TNS.2008.2009448	journal	June 2009
Experiences with making diffraction image data available: what metadata do we need to archive? Kroon-Batenburg, Loes M. J.; Helliwell, John R. Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 10 https://doi.org/10.1107/S1399004713029817	journal	September 2014
Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian IUCrJ, Vol. 4, Issue 1 https://doi.org/10.1107/S2052252516018315	journal	January 2017
McStas, a general software package for neutron ray-tracing simulations Lefmann, Kim; Nielsen, Kristian Neutron News, Vol. 10, Issue 3 https://doi.org/10.1080/10448639908233684	journal	January 1999
JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography Leonarski, Filip; Mozzanica, Aldo; Brückner, Martin Structural Dynamics, Vol. 7, Issue 1 https://doi.org/10.1063/1.5143480	journal	January 2020
OnDA : online data analysis and feedback for serial X-ray imaging Mariani, Valerio; Morgan, Andrew; Yoon, Chun Hong Journal of Applied Crystallography, Vol. 49, Issue 3 https://doi.org/10.1107/S1600576716007469	journal	May 2016
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
From then till now: changing data collection methods in single crystal X-ray crystallography since 1912 Powell, Harold R. Crystallography Reviews, Vol. 25, Issue 4 https://doi.org/10.1080/0889311X.2019.1615483	journal	June 2019
Operation and performance of the JUNGFRAU photon detector during first FEL and synchrotron experiments Redford, S.; Andrä, M.; Barten, R. Journal of Instrumentation, Vol. 13, Issue 11 https://doi.org/10.1088/1748-0221/13/11/C11006	journal	November 2018
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
xia2 : an expert system for macromolecular crystallography data reduction Winter, G. Journal of Applied Crystallography, Vol. 43, Issue 1 https://doi.org/10.1107/S0021889809045701	journal	December 2009
DIALS : implementation and evaluation of a new integration package Winter, Graeme; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2 https://doi.org/10.1107/S2059798317017235	journal	February 2018
Predicting the X-ray lifetime of protein crystals Zeldin, O. B.; Brockhauser, S.; Bremridge, J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 51 https://doi.org/10.1073/pnas.1315879110	journal	December 2013

Similar Records

Gold Standard for macromolecular crystallography diffraction data

Journal Article · 2020 · IUCrJ · OSTI ID:1638110

Bernstein, Herbert J.; Förster, Andreas; Bhowmick, Asmit; +9 more

Massive compression for high data rate macromolecular crystallography (HDRMX): impact on diffraction data and subsequent structural analysis

Journal Article · 2025 · Journal of Synchrotron Radiation (Online) · OSTI ID:2512413

Bernstein, Herbert J.; Soares, Alexei S.; Horvat, Kimberly; +1 more

Related Subjects

99 GENERAL AND MISCELLANEOUS

68 image lysozyme dataset recorded on the Jungfrau 16M detector at SwissFEL and formatted as a NeXus file Brewster, Aaron; Wang, Meitian; Bernstein, Herbert J. https://doi.org/10.5281/zenodo.3352357 The current record is supplemented by this dataset	dataset	January 2019
Small example Eiger 2X 16M data set from Diamond Light Source I04 revised for HDRMX Gold Standard Discussion Winter, Graeme; Brewster, Aaron; Bernstein, Herbert J. https://doi.org/10.5281/zenodo.3484186 The current record is supplemented by this dataset	dataset	January 2019
Small example Eiger 2X 16M data set from Diamond Light Source I04 revised for HDRMX Gold Standard Discussion Winter, Graeme; Brewster, Aaron; Bernstein, Herbert J. https://doi.org/10.5281/zenodo.3484187 The current record is supplemented by this dataset	dataset	January 2019

Gold Standard for macromolecular crystallography diffraction data

Citation Formats

References (30)

Linked Research (3)

Similar Records

Related Subjects