Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement.

Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.

Keywords

Patterson correlation refinement, antibodies, crystallographic phasing, fragment-based molecular replacement, maximum likelihood, Crystallography, X-Ray, Databases, Protein, Humans, Immunoglobulin Fab Fragments, Likelihood Functions, Models, Molecular, Protein Conformation, Rotation, Software

Journal Title

Acta Crystallogr D Struct Biol

Journal ISSN

2059-7983
2059-7983

Volume Title

74

Publisher

International Union of Crystallography (IUCr)

Publisher DOI

https://doi.org/10.1107/S2059798318001353

Rights and licensing

Except where otherwised noted, this item's license is described as Attribution 4.0 International

Sponsorship

Biotechnology and Biological Sciences Research Council (BB/L006014/1)
Wellcome Trust (082961/Z/07/A)
STFC
National Institutes of Health (NIH) (via University of California) (6801943)
National Institutes of Health (NIH) (via University of California) (6801943)
Wellcome Trust (082961/Z/07/Z)
National Institute of General Medical Sciences (P01GM063210)
Wellcome Trust (209407/Z/17/Z)

Collections

University of Cambridge Research Outputs (Articles and Conferences)