Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

Brunger, A.T.; Das, D.; Deacon, A.M.; Grant, J.; Terwilliger, T.C.; Read, R.J.; Adams, P.D.; Levitt, M.; Schröder, G.F.

doi:10.1107/S090744491104978X

Figure 5
Comparison of various refinements and maps for residues 251–276. Residues 251–263 comprising an α-helix, residues 264–271 comprising a loop and residues 272–276 comprising a β-strand are shown (the sequence numbers refer to the genomic sequence; see Fig. 1

). (a) Standard refinement (gray) versus the final model (orange). Standard refinement produces fragmented or incorrectly connected electron density (marked by arrows). (b) Standard refinement and one round of AutoBuild (blue) versus the final model (orange). Electron density is still fragmented or shows incorrect connectivity. (c) DEN refinement (green) versus the final model (orange). (d) DEN refinement and one round of AutoBuild (magenta) versus the result of semi-automated rebuilding (yellow). (e) 2mF_o − DF_c electron-density map after standard refinement (blue mesh) and a subsequent round of AutoBuild (cyan mesh) versus the final structure (orange sticks). (f) 2mF_o − DF_c electron-density map after DEN refinement (blue) and a subsequent round of AutoBuild (cyan) versus the final structure (orange sticks). (g) Electron-density map obtained by density modification of the MAD map (blue) versus the final structure (orange sticks). (h) 2mF_o − DF_c electron-density map (blue mesh) of the final model (orange sticks).

STRUCTURAL
BIOLOGY

ISSN: 2059-7983

Volume 68| Part 4| April 2012| Pages 391-403

https://doi.org/10.1107/S090744491104978X

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