Biological Crystallography Experimental Phasing with Shelxc/d/e: Combining Chain Tracing with Density Modification

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A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO. (2017, methodology): “…DNA pDEST15 N/A Software and Algorithms Phenix Adams et al., 2010 https://www.phenix-online.org/ Coot Emsley et al., 2010 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ CpHMD Mongan et al., 2004 N/A MOLProbity Chen et al., 2010 http://molprobity.biochem.duke.edu/ Other Structure.”
Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex (2015, methodology): “Chen VB, et al. (2010) MolProbity: All-atom structure validation for macromolecular crystallography.”
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures (2019, background): “(29) on the correlation between the sugar puckering and the perpendicular distance between the bridging P atom and the preceding C1′–N1/9 glycosidic bond, we extended the 3DNA double-helical parameter Zp (30) to a single-stranded analog (ssZp).”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “Clashscores, in particular, are observed to be elevated when using NCS restraints, particularly in cases where there are still a significant percentage of uncorrected rotamer outliers, where the increased rigidity introduced through torsion restraints prevents these errors from being distributed acr”