 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 3]](wd5088fig3_combined_mag.jpg)
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Figure 3
σA-weighted (2mFo − DFc)exp(iφc) and OMIT maps for 1zen (Cooper et al., 1996  ) compared with the structure 1zen
and that of chain A from 1b57
(Hall et al., 1999) superimposed on the structure 1zen
. Maps are contoured at 1σ. (a, b) σA-weighted (2mFo − DFc)exp(iφc) map (Read, 1986) calculated after refinement of the 1zen
structure with phenix.refine (Afonine et al., 2005b), compared with structure of 1zen
(a) and with chain A from 1b57
(b). (c, d) As in (a) and (b), except that the atoms in the 1zen
structure were moved randomly by an r.m.s. distance of 1 Å (`shake' procedure) and then refined for six cycles with phenix.refine. (e, f) As in (c) and (d), except that solvent water molecules were removed after the shake procedure and ten cycles of refinement including simulated annealing were carried out. (g, h) As in (a) and (b), except the map shown is a simple OMIT map calculated by omitting all atoms in an OMIT box with edges parallel to the cell edges and 4 Å from any atom in residues 5–9 of 1zen
(setting their occupancies to zero), refining the resulting structure and calculating a σA-weighted (2mFo − DFc)exp(iφc) map. (i, j) Map calculated as in (g) and (h) except the map is a simulated-annealing OMIT map in which the refinement step in (c) and (d) is replaced by simulated-annealing refinement (Brünger et al., 1998). (k, l) Iterative-build OMIT map calculated as in (g) and (h) except that the 1zen
structure was iteratively rebuilt using the rebuild-in-place option of the PHENIX AutoBuild Wizard, always setting the occupancies of all atoms in the OMIT box to zero during the procedure. (m, n) Maps downloaded from the EDS density server (Kleywegt et al., 2004). (m) σA-weighted (2mFo − DFc)exp(iφc) map and model for 1zen
. (n) σA-weighted (mFo − DFc)exp(iφc) map for 1zen
contoured at ±2σ with coordinates of 1zen
(green) and 1b57
(blue) superimposed. |
![[Figure 3]](wd5088fig3_combined.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
