title: Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing.
abstract: A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. A simple theoretical framework for describing measurements of anomalous differences and the resulting useful anomalous correlation and anomalous signal in a SAD experiment is presented. Here, the useful anomalous correlation is defined as the correlation of anomalous differences with ideal anomalous differences from the anomalous substructure. The useful anomalous correlation reflects the accuracy of the data and the absence of minor sites. The useful anomalous correlation also reflects the information available for estimating crystallographic phases once the substructure has been determined. In contrast, the anomalous signal (the peak height in a model-phased anomalous difference Fourier at the coordinates of atoms in the anomalous substructure) reflects the information available about each site in the substructure and is related to the ability to find the substructure. A theoretical analysis shows that the expected value of the anomalous signal is the product of the useful anomalous correlation, the square root of the ratio of the number of unique reflections in the data set to the number of sites in the substructure, and a function that decreases with increasing values of the atomic displacement factor for the atoms in the substructure. This means that the ability to find the substructure in a SAD experiment is increased by high data quality and by a high ratio of reflections to sites in the substructure, and is decreased by high atomic displacement factors for the substructure.
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Terwilliger
authors.affiliation: Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England.
authors.forename: Gábor
authors.initials: G
authors.lastname: Bunkóczi
authors.affiliation: Physics Division, Los Alamos National Laboratory, Mail Stop D454, Los Alamos, NM 87545, USA.
authors.forename: Li Wei
authors.initials: LW
authors.lastname: Hung
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Zwart
authors.affiliation: Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Janet L
authors.initials: JL
authors.lastname: Smith
authors.affiliation: Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Akey
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
mesh_terms: D000465:Algorithms; D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D059629:Signal-To-Noise Ratio; D012984:Software
chemical_list: D011506:Proteins
keywords: SAD phasing; anomalous phasing; anomalous signal; solving structures