title: Experimental phasing: best practice and pitfalls.
abstract: Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional notions of the composition of the substructure and the best coefficients for map generation are discussed. Pitfalls such as determining the enantiomorph, identifying centrosymmetry (or pseudo-symmetry) in the substructure and crystal twinning are discussed in detail. An appendix introduces combined real-imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the software Phaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods.
authors.affiliation: Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 OXY, England. ajm201@cam.ac.uk
authors.forename: Airlie J
authors.initials: AJ
authors.lastname: McCoy
authors.forename: Randy J
authors.initials: RJ
authors.lastname: Read
mesh_terms: D018360:Crystallography, X-Ray / Q000379:methods*; D011336:Probability; D011506:Proteins / Q000032:analysis*; D012984:Software
chemical_list: D011506:Proteins
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