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Article: Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering

TitleImplementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering
Authors
Issue Date2000
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, 2000, v. 56 n. 8, p. 1002-1006 How to Cite?
AbstractSolution of the phase problem is central to crystallographic structure determination. The conventional methods of isomorphous replacement (MIR or SIR) and molecular replacement are ineffective in the absence of a suitable isomorphous heavy-atom derivative or knowledge of the structure of a homologous protein. A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has shown to be successful in locating the molecular shape within the crystallographic unit cell in the case of the trimer nitrite reductase (NiR, 105 kDa) [Hao et al. (1999), Acta Cryst. D55, 243-246]. This was achieved by performing a direct real-space search for orientation and translation using knowledge of the orientation of the polar angles of the non-crystallographic axis obtained by performing a self-rotation on crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle γ and three translational parameters). In the case of NiR, the direct four-dimensional search produced a clear solution that was in good agreement with the known structure. The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups and in particular those in possession of non-crystallographic symmetry. However, the method employed was initially unsuccessful when applied to the small dimeric molecule superoxide dismutase (SOD, 32 kDa) owing to the absence of strong reflections at low resolution caused by saturation at the detector. The determined solution deviated greatly from that of the known structure [Hough and Hasnain (1999), J. Mol. Biol. 287, 579-592]. It was found that once these absent reflections were replaced by a series of randomly generated intensity values and cluster analysis was performed on the output, the signal-to-noise ratio was improved and a most probable solution was found. The electron-density map of the stochastically determined solution agrees well with the known structure; the phase error calculated from this map was 67°within 14 Å resolution.
Persistent Identifierhttp://hdl.handle.net/10722/91899
ISSN
2013 Impact Factor: 7.232
2015 SCImago Journal Rankings: 3.088
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorOckwell, DMen_HK
dc.contributor.authorHough, MAen_HK
dc.contributor.authorGrossmann, JGen_HK
dc.contributor.authorHasnain, SSen_HK
dc.contributor.authorHao, Qen_HK
dc.date.accessioned2010-09-17T10:29:56Z-
dc.date.available2010-09-17T10:29:56Z-
dc.date.issued2000en_HK
dc.identifier.citationActa Crystallographica Section D: Biological Crystallography, 2000, v. 56 n. 8, p. 1002-1006en_HK
dc.identifier.issn0907-4449en_HK
dc.identifier.urihttp://hdl.handle.net/10722/91899-
dc.description.abstractSolution of the phase problem is central to crystallographic structure determination. The conventional methods of isomorphous replacement (MIR or SIR) and molecular replacement are ineffective in the absence of a suitable isomorphous heavy-atom derivative or knowledge of the structure of a homologous protein. A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has shown to be successful in locating the molecular shape within the crystallographic unit cell in the case of the trimer nitrite reductase (NiR, 105 kDa) [Hao et al. (1999), Acta Cryst. D55, 243-246]. This was achieved by performing a direct real-space search for orientation and translation using knowledge of the orientation of the polar angles of the non-crystallographic axis obtained by performing a self-rotation on crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle γ and three translational parameters). In the case of NiR, the direct four-dimensional search produced a clear solution that was in good agreement with the known structure. The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups and in particular those in possession of non-crystallographic symmetry. However, the method employed was initially unsuccessful when applied to the small dimeric molecule superoxide dismutase (SOD, 32 kDa) owing to the absence of strong reflections at low resolution caused by saturation at the detector. The determined solution deviated greatly from that of the known structure [Hough and Hasnain (1999), J. Mol. Biol. 287, 579-592]. It was found that once these absent reflections were replaced by a series of randomly generated intensity values and cluster analysis was performed on the output, the signal-to-noise ratio was improved and a most probable solution was found. The electron-density map of the stochastically determined solution agrees well with the known structure; the phase error calculated from this map was 67°within 14 Å resolution.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.titleImplementation of cluster analysis for ab initio phasing using the 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/S0907444900007721en_HK
dc.identifier.pmid10944337-
dc.identifier.scopuseid_2-s2.0-0033883994en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0033883994&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume56en_HK
dc.identifier.issue8en_HK
dc.identifier.spage1002en_HK
dc.identifier.epage1006en_HK
dc.identifier.isiWOS:000088384200009-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridOckwell, DM=6602777714en_HK
dc.identifier.scopusauthoridHough, MA=7005810382en_HK
dc.identifier.scopusauthoridGrossmann, JG=7005976005en_HK
dc.identifier.scopusauthoridHasnain, SS=7102767936en_HK
dc.identifier.scopusauthoridHao, Q=7102508868en_HK

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