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A general method for directly phasing diffraction data from high-solvent-content protein crystals
A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction p...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9438493/ https://www.ncbi.nlm.nih.gov/pubmed/36071801 http://dx.doi.org/10.1107/S2052252522006996 |
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author | Kingston, Richard Lawrence Millane, Rick P. |
author_facet | Kingston, Richard Lawrence Millane, Rick P. |
author_sort | Kingston, Richard Lawrence |
collection | PubMed |
description | A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction problem, in which an image is sought that is consistent with both the diffraction data and generic constraints on the density distribution in the crystal. The problem is solved using an iterative projection algorithm, the Difference Map algorithm, which has good global convergence properties, and can locate the correct solution without any initial phase information. Computational efficiency is improved by breaking the problem down into two stages; initial approximation of the molecular envelope at low resolution, followed by subsequent phase determination using all of the data. The molecular envelope is continually updated during the phase determination step. At both stages, the algorithm is initiated with many different and random phase sets, which are evolved subject to the constraints. A clustering procedure is used to identify consistent results across multiple runs, which are then averaged to generate consensus envelopes or phase sets. The emergence of highly consistent phase sets is diagnostic of success. The effectiveness of the procedure is demonstrated by application to 42 known structures of solvent fraction 0.60–0.85. The procedure works robustly at intermediate resolutions (1.9–3.5 Å) but is strongly dependent on crystal solvent content, only working routinely with solvent fractions greater than 0.70. |
format | Online Article Text |
id | pubmed-9438493 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-94384932022-09-06 A general method for directly phasing diffraction data from high-solvent-content protein crystals Kingston, Richard Lawrence Millane, Rick P. IUCrJ Research Papers A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction problem, in which an image is sought that is consistent with both the diffraction data and generic constraints on the density distribution in the crystal. The problem is solved using an iterative projection algorithm, the Difference Map algorithm, which has good global convergence properties, and can locate the correct solution without any initial phase information. Computational efficiency is improved by breaking the problem down into two stages; initial approximation of the molecular envelope at low resolution, followed by subsequent phase determination using all of the data. The molecular envelope is continually updated during the phase determination step. At both stages, the algorithm is initiated with many different and random phase sets, which are evolved subject to the constraints. A clustering procedure is used to identify consistent results across multiple runs, which are then averaged to generate consensus envelopes or phase sets. The emergence of highly consistent phase sets is diagnostic of success. The effectiveness of the procedure is demonstrated by application to 42 known structures of solvent fraction 0.60–0.85. The procedure works robustly at intermediate resolutions (1.9–3.5 Å) but is strongly dependent on crystal solvent content, only working routinely with solvent fractions greater than 0.70. International Union of Crystallography 2022-08-13 /pmc/articles/PMC9438493/ /pubmed/36071801 http://dx.doi.org/10.1107/S2052252522006996 Text en © Kingston and Millane 2022 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
spellingShingle | Research Papers Kingston, Richard Lawrence Millane, Rick P. A general method for directly phasing diffraction data from high-solvent-content protein crystals |
title | A general method for directly phasing diffraction data from high-solvent-content protein crystals |
title_full | A general method for directly phasing diffraction data from high-solvent-content protein crystals |
title_fullStr | A general method for directly phasing diffraction data from high-solvent-content protein crystals |
title_full_unstemmed | A general method for directly phasing diffraction data from high-solvent-content protein crystals |
title_short | A general method for directly phasing diffraction data from high-solvent-content protein crystals |
title_sort | general method for directly phasing diffraction data from high-solvent-content protein crystals |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9438493/ https://www.ncbi.nlm.nih.gov/pubmed/36071801 http://dx.doi.org/10.1107/S2052252522006996 |
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