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Article: Ab initio phasing using molecular envelope from solution X-ray scattering

TitleAb initio phasing using molecular envelope from solution X-ray scattering
Authors
Issue Date1999
PublisherWiley-Blackwell Publishing, Inc.. The Journal's web site is located at http://www.wiley.com/bw/editors.asp?ref=0907-4449&site=1
Citation
Acta Crystallographica Section D: Biological Crystallography, 1999, v. 55 n. 1, p. 243-246 How to Cite?
AbstractSolving the phase problem is the crucial and quite often the most difficult and time-consuming step in crystallographic structure determination. The traditional methods of isomorphous replacement (MIR or SIR) and molecular replacement require the availability of an isomorphous heavy-atom derivative or the structure of a homologous protein, respectively. Here, a method is presented which utilizes the low-resolution molecular shape determined from solution X-ray scattering data for the molecular search. The molecular shape of a protein is an important structural property and can be determined directly by the small-angle scattering technique. The idea of locating this molecular shape in the crystallographic unit cell has been tested with experimental diffraction data from nitrite reductase (NiR). The conventional Patterson search proved to be unsuccessful, as the intra-envelope vectors are uniformly distributed and do not match those of intra-molecular (atom-to-atom) vectors. A direct real-space search for orientation and translation was then performed. A self-rotation function using 2.8 Å crystallographic data yielded the polar angles of the non-crystallographic threefold axis. Knowledge of the orientation of this axis reduces the potential six-dimensional search to four (Eulerian angle γ and three translational parameters). The direct four-dimensional search within the unit cell produced a clear solution. The electron-density map based on this solution agrees well with the known structure, and the phase error calculated from the map was 61 °within 20 Å resolution. It is anticipated that the low-resolution envelope can be used as a starting model for phase extension by the maximum-entropy and density-modification method.
Persistent Identifierhttp://hdl.handle.net/10722/91919
ISSN
2013 Impact Factor: 7.232
2015 SCImago Journal Rankings: 3.088
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorHao, Qen_HK
dc.contributor.authorDodd, FEen_HK
dc.contributor.authorGrossmann, JGen_HK
dc.contributor.authorHasnain, SSen_HK
dc.date.accessioned2010-09-17T10:30:32Z-
dc.date.available2010-09-17T10:30:32Z-
dc.date.issued1999en_HK
dc.identifier.citationActa Crystallographica Section D: Biological Crystallography, 1999, v. 55 n. 1, p. 243-246en_HK
dc.identifier.issn0907-4449en_HK
dc.identifier.urihttp://hdl.handle.net/10722/91919-
dc.description.abstractSolving the phase problem is the crucial and quite often the most difficult and time-consuming step in crystallographic structure determination. The traditional methods of isomorphous replacement (MIR or SIR) and molecular replacement require the availability of an isomorphous heavy-atom derivative or the structure of a homologous protein, respectively. Here, a method is presented which utilizes the low-resolution molecular shape determined from solution X-ray scattering data for the molecular search. The molecular shape of a protein is an important structural property and can be determined directly by the small-angle scattering technique. The idea of locating this molecular shape in the crystallographic unit cell has been tested with experimental diffraction data from nitrite reductase (NiR). The conventional Patterson search proved to be unsuccessful, as the intra-envelope vectors are uniformly distributed and do not match those of intra-molecular (atom-to-atom) vectors. A direct real-space search for orientation and translation was then performed. A self-rotation function using 2.8 Å crystallographic data yielded the polar angles of the non-crystallographic threefold axis. Knowledge of the orientation of this axis reduces the potential six-dimensional search to four (Eulerian angle γ and three translational parameters). The direct four-dimensional search within the unit cell produced a clear solution. The electron-density map based on this solution agrees well with the known structure, and the phase error calculated from the map was 61 °within 20 Å resolution. It is anticipated that the low-resolution envelope can be used as a starting model for phase extension by the maximum-entropy and density-modification method.en_HK
dc.languageengen_HK
dc.publisherWiley-Blackwell Publishing, Inc.. The Journal's web site is located at http://www.wiley.com/bw/editors.asp?ref=0907-4449&site=1en_HK
dc.relation.ispartofActa Crystallographica Section D: Biological Crystallographyen_HK
dc.titleAb initio phasing using molecular envelope from solution X-ray scatteringen_HK
dc.typeArticleen_HK
dc.identifier.emailHao, Q: qhao@hku.hken_HK
dc.identifier.authorityHao, Q=rp01332en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1107/s0907444998011342en_US
dc.identifier.pmid10089416-
dc.identifier.scopuseid_2-s2.0-13044258870en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-13044258870&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume55en_HK
dc.identifier.issue1en_HK
dc.identifier.spage243en_HK
dc.identifier.epage246en_HK
dc.identifier.isiWOS:000078314000030-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridHao, Q=7102508868en_HK
dc.identifier.scopusauthoridDodd, FE=7004001288en_HK
dc.identifier.scopusauthoridGrossmann, JG=7005976005en_HK
dc.identifier.scopusauthoridHasnain, SS=7102767936en_HK

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