Combining phase information in reciprocal space for molecular replacement with partial models

Acta Crystallographica. Section D, Biological Crystallography
Claudia MillánIsabel Usón

Abstract

ARCIMBOLDO allows ab initio phasing of macromolecular structures below atomic resolution by exploiting the location of small model fragments combined with density modification in a multisolution frame. The model fragments can be either secondary-structure elements predicted from the sequence or tertiary-structure fragments. The latter can be derived from libraries of typical local folds or from related structures, such as a low-homology model that is unsuccessful in molecular replacement. In all ARCIMBOLDO applications, fragments are searched for sequentially. Correct partial solutions obtained after each fragment-search stage but lacking the necessary phasing power can, if combined, succeed. Here, an analysis is presented of the clustering of partial solutions in reciprocal space and of its application to a set of different cases. In practice, the task of combining model fragments from an ARCIMBOLDO run requires their referral to a common origin and is complicated by the presence of correct and incorrect solutions as well as by their not being independent. The F-weighted mean phase difference has been used as a figure of merit. Clustering perfect, non-overlapping fragments dismembered from test structures in polar and nonpolar...Continue Reading

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Citations

Sep 1, 2016·Acta Crystallographica. Section A, Foundations and Advances·Hongxing HeWu Pei Su
Apr 14, 2018·Acta Crystallographica. Section D, Structural Biology·Claudia MillánIsabel Usón
Apr 14, 2018·Acta Crystallographica. Section D, Structural Biology·Robert D OeffnerAirlie J McCoy
Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Claudia MillánIsabel Usón
Aug 4, 2020·Acta Crystallographica. Section D, Structural Biology·Logan S RichardsJose A Rodriguez
Jun 20, 2018·Nature Structural & Molecular Biology·James M DunceOwen R Davies
Aug 17, 2019·The Journal of Biological Chemistry·Natalie C BamfordP Lynne Howell

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