Literature DB >> 31934601

Best practices for high data-rate macromolecular crystallography (HDRMX).

Herbert J Bernstein1, Lawrence C Andrews2, Jorge A Diaz1, Jean Jakoncic3, Thu Nguyen4, Nicholas K Sauter5, Alexei S Soares3, Justin Y Wei6, Maciej R Wlodek4, Mario A Xerri6.   

Abstract

In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem-improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.
© 2020 Author(s).

Entities:  

Year:  2020        PMID: 31934601      PMCID: PMC6952294          DOI: 10.1063/1.5128498

Source DB:  PubMed          Journal:  Struct Dyn        ISSN: 2329-7778            Impact factor:   2.920


  18 in total

1.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

2.  Robust indexing for automatic data collection.

Authors:  Nicholas K Sauter; Ralf W Grosse-Kunstleve; Paul D Adams
Journal:  J Appl Crystallogr       Date:  2004-05-11       Impact factor: 3.304

Review 3.  Scaling and assessment of data quality.

Authors:  Philip Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

4.  Dissecting random and systematic differences between noisy composite data sets.

Authors:  Kay Diederichs
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-03-31       Impact factor: 7.652

5.  Automated data collection and real-time data analysis suite for serial synchrotron crystallography.

Authors:  Shibom Basu; Jakub W Kaminski; Ezequiel Panepucci; Chia Ying Huang; Rangana Warshamanage; Meitian Wang; Justyna Aleksandra Wojdyla
Journal:  J Synchrotron Radiat       Date:  2019-01-01       Impact factor: 2.616

6.  Selling reduction versus Niggli reduction for crystallographic lattices.

Authors:  Lawrence C Andrews; Herbert J Bernstein; Nicholas K Sauter
Journal:  Acta Crystallogr A Found Adv       Date:  2019-01-01       Impact factor: 2.290

7.  Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography.

Authors:  James Foadi; Pierre Aller; Yilmaz Alguel; Alex Cameron; Danny Axford; Robin L Owen; Wes Armour; David G Waterman; So Iwata; Gwyndaf Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-07-20

8.  Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity.

Authors:  Richard J Gildea; Graeme Winter
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-24       Impact factor: 7.652

9.  KAMO: towards automated data processing for microcrystals.

Authors:  Keitaro Yamashita; Kunio Hirata; Masaki Yamamoto
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-24       Impact factor: 7.652

10.  Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II.

Authors:  Michelle S Miller; Sweta Maheshwari; Wuxian Shi; Yuan Gao; Nam Chu; Alexei S Soares; Philip A Cole; L Mario Amzel; Martin R Fuchs; Jean Jakoncic; Sandra B Gabelli
Journal:  Molecules       Date:  2019-01-30       Impact factor: 4.411

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  4 in total

1.  Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources.

Authors:  Pierre Aller; Allen M Orville
Journal:  Methods Mol Biol       Date:  2021

Review 2.  Transactions from the 69th Annual Meeting of the American Crystallographic Association: Data best practices-current state and future needs.

Authors:  Nicholas K Sauter; John P Rose; Talapady N Bhat
Journal:  Struct Dyn       Date:  2020-03-24       Impact factor: 2.920

3.  A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs.

Authors:  Thu Nguyen; Kim L Phan; Dima Kozakov; Sandra B Gabelli; Dale F Kreitler; Lawrence C Andrews; Jean Jakoncic; Robert M Sweet; Alexei S Soares; Herbert J Bernstein
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-02-18       Impact factor: 7.652

4.  Gold Standard for macromolecular crystallography diffraction data.

Authors:  Herbert J Bernstein; Andreas Förster; Asmit Bhowmick; Aaron S Brewster; Sandor Brockhauser; Luca Gelisio; David R Hall; Filip Leonarski; Valerio Mariani; Gianluca Santoni; Clemens Vonrhein; Graeme Winter
Journal:  IUCrJ       Date:  2020-07-10       Impact factor: 4.769

  4 in total

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