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![[Figure 5]](qj5007fig5mag.jpg)
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Figure 5
(a) Plot showing the B factor from the original PDB file (grey) and the derived equivalent B factor from the Vagabond structure (black) per Cα atom. (b) Final R factors per resolution bin for REFMAC5 and Vagabond for the occupancy-corrected structure. Apart from an improvement at resolutions lower than 3.7 Å, Vagabond gives higher R factors throughout the rest of the resolution ranges. (c) After correcting occupancy values, density from the PDB-REDO model refined using REFMAC5 was overlaid on the structure (2mFo − DFc 1σ, Fo − Fc 3σ). (d) The PDB-REDO model refined in Vagabond produces new electron density, which is overlaid on the original model (2mFo − DFc, 1σ; Fo − Fc, 3σ). (e) Refitting of the model to Vagabond-derived electron density in Coot showing improved backbone fit against electron density (2Fo − Fc plus phase spread, Section 2 ![[link]](../../../../../../logos/arrows/d_arr.gif) , 1σ; Fo − Fc plus phase spread, 3σ). (c), (d) and (e) were drawn with Coot (Emsley et al., 2010) and Raster3D (Merritt & Bacon, 1997). (f) A Kleywegt plot drawn using Coot shows large movement of three residues, of which Lys10 switches from one minimum in the Ramachandran plot to another. |
![[Figure 5]](qj5007fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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