Solving structures of protein complexes by molecular replacement with Phaser

By A. McCoy. Acta Crystallographica Section D: Biological Crystallography, 2006

1,632 citations recorded by the source corpus.

Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a5d4c5efe29ea39c90bd12d01df6455538429c13

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Citations in the corpus

Crystal Structure of the β2Adrenergic Receptor-Gs protein complex (2011, neutral): “The structure was solved by molecular replacement using Phaser 39,40 .”
A Structural Basis for Antigen Presentation by the MHC Class Ib Molecule, Qa-1b (2012, methodology): “The crystal structure was solved by molecular replacement, as implemented in PHASER (36).”
Phaser crystallographic software (2007, methodology): “When searching for multiple copies of the same component in the asymmetric unit, several copies should be added at each search step (rather than branching at each search step), but this search strategy must currently be performed semi-manually as described elsewhere (McCoy, 2007).”
The Crystal Structures of Apo and cAMP-Bound GlxR from Corynebacterium glutamicum Reveal Structural and Dynamic Changes upon cAMP Binding in CRP/FNR Family Transcription Factors (2014, methodology): “Structure solution, refinement and analysis Crystal form II of cAMP-bound Cg-GlxR was first solved by molecular replacement with PHASER [40] using the structure of CRP from M.”
Recent developments in classical density modification (2010, methodology): “…correction to the data to enhance the structure factors along directions in which they are weaker (although this does not correct for an anisotropic resolution limit) and this technique has been applied effectively even without an atomic model in programs such as Phaser (McCoy, 2007; Read, 2008).”
On the application of the expected log-likelihood gain to decision making in molecular replacement (2018, methodology): “The BETA–BLIP structure (Strynadka et al., 1996), which has previously been used as a test case for Phaser (Storoni et al., 2004; McCoy et al., 2005; McCoy, 2007), was used to generate simulated data with different hemihedral twin fractions, and the LLGI was calculated for the structure given the…”
Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase From Shigella flexneri (2018, methodology): “The structures of Spa4711-83 in complex with ATP analogs, AMPPNP or ATPγS were solved by molecular replacement (McCoy, 2007) using the structures of unliganded Spa4711-83 as the searching models.”