Structure Determination of a Small Protein Through a 23-dimensional Molecular-replacement Search
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The crystal structure of a 4-alpha-helical bundle protein has been determined by the application of a 23-dimensional molecular-replacement search performed using a stochastic method. The search model for the calculation was a 26-residue-long polyalanine helix amounting to less than 13% of the total number of atoms in the asymmetric unit of the target crystal structure. The crystal structure determination procedure is presented in detail, with emphasis on the molecular-replacement calculations.
Vouzina O, Tafanidis A, Glykos N J Chem Inf Model. 2024; 64(15):6081-6091.
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Phasertng: directed acyclic graphs for crystallographic phasing.
McCoy A, Stockwell D, Sammito M, Oeffner R, Hatti K, Croll T Acta Crystallogr D Struct Biol. 2021; 77(Pt 1):1-10.
PMID: 33404520 PMC: 7787104. DOI: 10.1107/S2059798320014746.
SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.
Borges R, Meindl K, Trivino J, Sammito M, Medina A, Millan C Acta Crystallogr D Struct Biol. 2020; 76(Pt 3):221-237.
PMID: 32133987 PMC: 7057211. DOI: 10.1107/S2059798320000339.
On the application of the expected log-likelihood gain to decision making in molecular replacement.
Oeffner R, Afonine P, Millan C, Sammito M, Uson I, Read R Acta Crystallogr D Struct Biol. 2018; 74(Pt 4):245-255.
PMID: 29652252 PMC: 5892874. DOI: 10.1107/S2059798318004357.
Caballero I, Sammito M, Millan C, Lebedev A, Soler N, Uson I Acta Crystallogr D Struct Biol. 2018; 74(Pt 3):194-204.
PMID: 29533227 PMC: 5947760. DOI: 10.1107/S2059798317017582.