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Figure 6
(a) For PDB entry 5g5y, averaged weighted density over two copies in the asymmetric unit (mFo − DFc, 1σ), 0.7σ level, and difference density (Fo − Fc), 2.7σ level, for the PDB-REDO structure recalculated without water molecules. (b) Refinement with Vagabond from the initial PDB file without water molecules; averaged weighted density over two copies in the asymmetric unit (2Fo − Fc and phase spread, Section 2[link]), 0.7σ level, and difference density (Fo − Fc), 2.7σ level. (c) Methylguanine placed using Coot real-space refinement to demonstrate the fit to density. (a), (b) and (c) were drawn in Coot (Emsley et al., 2010BB11) and Raster3D (Merritt & Bacon, 1997BB22). (d) Plot showing B factors from the original PDB file (grey) and the derived equivalent B factors from the Vagabond structure (black) per Cα atom.

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Volume 77| Part 4| April 2021| Pages 424-437
https://doi.org/10.1107/S2059798321000826
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