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On the application of the expected LLG to decision making in molecular replacement

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McCoy, Airlie 

Abstract

olecular replacement phasing of macromolecular crystal structures is often fast, but if a molecular replacement solution is not immediately obtained, the crystallographer must judge whether to pursue molecular replacement or attempt experimental phasing as the quickest path to structure solution. The introduction of eLLG (expected log-likelihood gain (McCoy et al., 2017)) has given the crystallographer a powerful new tool to aid in making this decision. The eLLG is LLGI (log-likelihood gain on intensity (Read & McCoy, 2016)) expected from a correctly placed model. It is calculated as a sum over the reflections of a function dependent on the fraction of the scattering for which the model accounts, the estimated model coordinate error, and the measurement errors in the data. We show how eLLG is used to answer the question "Can I solve my structure by molecular replacement?" However, this is only the most obvious of the applications of eLLG. We also discuss how eLLG is used for determining search order, minimal data requirements for obtaining a molecular replacement solution using a given model, and for decision making in fragment-based molecular replacement, single-atom molecular replacement, and likelihood-guided model pruning.

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Acta Crystallographica Section D

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Wellcome Trust (082961/Z/07/A)
Biotechnology and Biological Sciences Research Council (BB/L006014/1)
National Institutes of Health (NIH) (via University of California) (6801943)
Robert D. Oeffnera, Pavel Afonineb, Claudia Millánc, Massimo Sammitoc, Isabel Usóncd, Randy J. Reada* and Airlie J. McCoye* aHaematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, Cambs, CB2 0XY, United Kingdom b Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA, 94720, United States cCrystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac, 15, Barcelona, 08028, Spain dICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, Barcelona, E-08003, Spain eHaematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, Cambs, CB20XY, United Kingdom Correspondence email: rjr27@cam.ac.uk; ajm201@cam.ac.uk Funding information Wellcome Trust (grant No. 082961/Z/07/Z to Randy J. Read); BBSRC (grant No. BB/L006014/1 to Randy J. Read; bursary No. BB/L006014/1 to Claudia Millán, Massimo Sammito); Spanish Ministry of Economy and Competitiveness (grant No. BIO2015-64216-P to Isabel Usón; grant No. BIO2013-49604-EXP to Isabel Usón; grant No. MDM2014-0435-01 to Isabel Usón; scholarship No. BES-2015-071397 to Claudia Millán).