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Identification of rogue datasets in serial crystallography

Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completene...

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Autores principales: Assmann, Greta, Brehm, Wolfgang, Diederichs, Kay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886987/
https://www.ncbi.nlm.nih.gov/pubmed/27275144
http://dx.doi.org/10.1107/S1600576716005471
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author Assmann, Greta
Brehm, Wolfgang
Diederichs, Kay
author_facet Assmann, Greta
Brehm, Wolfgang
Diederichs, Kay
author_sort Assmann, Greta
collection PubMed
description Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC(1/2) [Karplus & Diederichs (2012 ▸). Science, 336, 1030–1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC(1/2) that avoids the random assignment, and instead of using an overall CC(1/2), an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested.
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spelling pubmed-48869872016-06-06 Identification of rogue datasets in serial crystallography Assmann, Greta Brehm, Wolfgang Diederichs, Kay J Appl Crystallogr Research Papers Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC(1/2) [Karplus & Diederichs (2012 ▸). Science, 336, 1030–1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC(1/2) that avoids the random assignment, and instead of using an overall CC(1/2), an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested. International Union of Crystallography 2016-04-18 /pmc/articles/PMC4886987/ /pubmed/27275144 http://dx.doi.org/10.1107/S1600576716005471 Text en © Greta Assmann et al. 2016 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Assmann, Greta
Brehm, Wolfgang
Diederichs, Kay
Identification of rogue datasets in serial crystallography
title Identification of rogue datasets in serial crystallography
title_full Identification of rogue datasets in serial crystallography
title_fullStr Identification of rogue datasets in serial crystallography
title_full_unstemmed Identification of rogue datasets in serial crystallography
title_short Identification of rogue datasets in serial crystallography
title_sort identification of rogue datasets in serial crystallography
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886987/
https://www.ncbi.nlm.nih.gov/pubmed/27275144
http://dx.doi.org/10.1107/S1600576716005471
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