Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

Terwilliger, Thomas C.; Bunkóczi, Gábor; Hung, Li-Wei; Zwart, Peter H.; Smith, Janet L.; Akey, David L.; Adams, Paul D.

doi:10.1107/S2059798315019403

Title: Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

Journal Article · Tue Mar 01 00:00:00 EST 2016 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S2059798315019403· OSTI ID:1254848

Terwilliger, Thomas C. ^[1]; Bunkóczi, Gábor ^[2]; Hung, Li-Wei ^[1]; Zwart, Peter H. ^[3]; Smith, Janet L. ^[4]; Akey, David L. ^[4]; Adams, Paul D. ^[3]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Univ. of Cambridge (United Kingdom)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Michigan, Ann Arbor, MI (United States)

A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. Here, algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment are described. A simple theoretical framework [Terwilligeret al.(2016),Acta Cryst.D72, 346–358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. Thephenix.plan_sad_experimenttool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimate the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. Thephenix.scale_and_mergetool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and thephenix.anomalous_signaltool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC)

Grant/Contract Number:: AC52-06NA25396; AC02-05CH11231; P01GM063210; P01AI055672

OSTI ID:: 1254848

Alternate ID(s):: OSTI ID: 1378774

Report Number(s):: LA-UR-15-22792; ACSDAD; PII: S2059798315019403

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Vol. 72, Issue 3; ISSN 2059-7983

Publisher:: IUCrCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 23 works

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59 BASIC BIOLOGICAL SCIENCES
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experimental design

Title: Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

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