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![[Figure 10]](jm5003fig10mag.jpg)
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Figure 10
Ligands placed into density of mother-liquor components. In the structure of Bacillus cereus chitinase (PDB entry 3n1a; Hsieh et al., 2010  ), the cyclo-(L-His-L-Pro) molecule (CHQ-1514, chain A) is placed into low-level electron density that is difficult to interpret (a) and which may be plausibly interpreted as an acetate molecule present in the crystallization cocktail at 200 mM, supported by a newly formed hydrogen bond between Asp-143 and the suggested acetate (b). In the structure of penicillin-binding protein 4 from Staphylococcus aureus (PDB entry 3hun; Navratna et al., 2010) the phenyl moiety of the ampicillin (ZZ7-501, chain B) is placed in a region of the electron density that based on difference density analysis could be better interpreted as a sulfate ion (c). The re-refined model that includes sulfate ion is shown in (d). (e) The original, obsoleted and distorted bacteriochlorophyll model at the eighth binding site in the FMO protein from Pelodictyon phaeum (PDB entry 3oeg); (f) depicts the same region of the corrected PDB entry 3vdi (Tronrud & Allen, 2012) modelled with more plausible PEG fragments and water molecules. Electron-density maps in (a), (b), (c) and (d) are 2.0 Å resolution mFo − DFc OMIT difference maps contoured at ±3σ (green/red) and 2mFo − DFc REFMAC maximum-likelihood OMIT maps contoured at 1σ (blue). The maps shown in (e) and (f) are positive difference density OMIT mFo − DFc maps (3σ level, blue) after BUSTER-TNT refinement following rebuilding of the structure with phenix.autobuild without any ligand included. (a), (b), (c) and (d) are modified from Pozharski et al. (2013); (e) and (f) were kindly supplied by Dale Tronrud, Department of Biochemistry and Biophysics, Oregon State University, USA. |
![[Figure 10]](jm5003fig10.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
