Structure and refinement of oxymyoglobin at 1.6 A resolution.

By Simon E. V. Phillips. 1980

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “…Grosse-Kunstleve & Adams, 2002), h is a column vector with the Miller indices of a reflection and ht is its transpose, Fcalc are the structure factors computed from the atomic model, ksol and Bsol are flat bulk-solvent model parameters (Phillips, 1980; 354 Afonine et al. phenix.refine Acta Cryst.”
Flat bulk-solvent model: obtaining optimal parameters. (2002, background): “The ¯at bulk-solvent model (Phillips, 1980; Jiang & BruÈ nger, 1994) is more reliable because it is based on the more reasonable assumption that the electron density in the solvent region has a uniform distribution.”
Averaged kick maps: less noise, more signal…and probably less bias (2009, methodology): “…correction models have been developed in order to be able to include all reflections in the map calculation rather than applying a low-resolution truncation (Moews & Kretsinger, 1975; Phillips, 1980; Jiang & Brünger, 1994; Tronrud, 1997; Badger, 1997; Urzhumtsev, 2000; Fokine & Urzhumtsev, 2002).”
X-ray structure determination at low resolution (2009, methodology): “To compute F bulk , one approach is to create a mask in order to distinguish between macromolecular and solvent regions (Brunger, 2007; Jiang & Brü nger, 1994; Phillips, 1980).”
Version 1.2 of the Crystallography and NMR system (2007, methodology): “The widely used 'flat' solvent model assumes that solvent regions outside the molecular surface show relatively little variation in density as compared to the macromolecul”
Bulk-solvent and overall scaling revisited: faster calculations, improved results (2013, methodology): “…modify (7) by adding the constant kanisotropic ¼ 1þ stV0sþ ðstV1sÞs2: ð9Þ The bulk-solvent scale factor is traditionally defined as kmask ¼ ksol expð Bsols2=4Þ; ð10Þ where ksol and Bsol are the flat bulk-solvent model parameters (Phillips, 1980; Jiang & Brünger, 1994; Fokine & Urzhumtsev, 2002b).”
Polder maps: improving OMIT maps by excluding bulk solvent (2017, methodology): “The areas of the unit cell that are not interpreted in terms of an atomic model are filled with the bulk solvent by constructing a binary mask set to 0 inside the atomic model and 1 elsewhere (Phillips, 1980; Fokine & Urzhumtsev, 2002; Afonine et al., 2005; Weichenberger et al., 2015).”
Metrics for comparison of crystallographic maps (2014, methodology): “It is largely accepted that using a bulk-solvent correction is vital in order to properly include low-resolution data into the structure-solution process (see, for example, Phillips, 1980; Fenn et al., 2010; Afonine et al., 2013 and references therein).”