title: Using SAD data in Phaser.
abstract: Phaser is a program that implements likelihood-based methods to solve macromolecular crystal structures, currently by molecular replacement or single-wavelength anomalous diffraction (SAD). SAD phasing is based on a likelihood target derived from the joint probability distribution of observed and calculated pairs of Friedel-related structure factors. This target combines information from the total structure factor (primarily non-anomalous scattering) and the difference between the Friedel mates (anomalous scattering). Phasing starts from a substructure, which is usually but not necessarily a set of anomalous scatterers. The substructure can also be a protein model, such as one obtained by molecular replacement. Additional atoms are found using a log-likelihood gradient map, which shows the sites where the addition of scattering from a particular atom type would improve the likelihood score. An automated completion algorithm adds new sites, choosing optionally among different atom types, adds anisotropic B-factor parameters if appropriate and deletes atoms that refine to low occupancy. Log-likelihood gradient maps can also identify which atoms in a refined protein structure are anomalous scatterers, such as metal or halide ions. These maps are more sensitive than conventional model-phased anomalous difference Fouriers and the iterative completion algorithm is able to find a significantly larger number of convincing sites.
authors: CIMR Haematology, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, England. rjr27@cam.ac.uk
authors: Randy J
authors: RJ
authors: Read
authors: Airlie J
authors: AJ
authors: McCoy
mesh_terms: D018360:Crystallography, X-Ray / Q000379:methods*; D011336:Probability; D011506:Proteins / Q000032:analysis*; D012984:Software
chemical_list: D011506:Proteins