A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures

The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489–493] improves its phasing efficiency for larger crystal structures with atomic reso...

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Detalles Bibliográficos
Autores: Rius, Jordi, Torrelles, Xavier
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/246767
Acceso en línea:http://hdl.handle.net/10261/246767
Access Level:acceso abierto
Palabra clave:SM phasing algorithm
ipp procedure
Structure solution
Direct methods
Origin-free modulus sum function
|ρ|-based phasing residual
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spelling A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structuresRius, JordiTorrelles, XavierSM phasing algorithmipp procedureStructure solutionDirect methodsOrigin-free modulus sum function|ρ|-based phasing residualThe incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489–493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.The following funding is acknowledged: MINECO and FEDER (grant No. RTI2018-098537-B-C21); Severo Ochoa Programme for Centres of Excellence in R&D (grant No. SEV-2015-0496).Peer reviewedInternational Union of CrystallographyMinisterio de Economía y Competitividad (España)European CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202120212021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/246767reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-098537-B-C21info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SEV-2015-0496http://dx.doi.org/10.1107/S2053273321004915Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2467672026-05-22T06:33:51Z
dc.title.none.fl_str_mv A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
title A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
spellingShingle A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
Rius, Jordi
SM phasing algorithm
ipp procedure
Structure solution
Direct methods
Origin-free modulus sum function
|ρ|-based phasing residual
title_short A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
title_full A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
title_fullStr A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
title_full_unstemmed A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
title_sort A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures
dc.creator.none.fl_str_mv Rius, Jordi
Torrelles, Xavier
author Rius, Jordi
author_facet Rius, Jordi
Torrelles, Xavier
author_role author
author2 Torrelles, Xavier
author2_role author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
European Commission
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv SM phasing algorithm
ipp procedure
Structure solution
Direct methods
Origin-free modulus sum function
|ρ|-based phasing residual
topic SM phasing algorithm
ipp procedure
Structure solution
Direct methods
Origin-free modulus sum function
|ρ|-based phasing residual
description The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489–493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/246767
url http://hdl.handle.net/10261/246767
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-098537-B-C21
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SEV-2015-0496
http://dx.doi.org/10.1107/S2053273321004915
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv International Union of Crystallography
publisher.none.fl_str_mv International Union of Crystallography
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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