Ligands placed into mother-liquor density. In the structure of Bacillus cereus chitinase, PDB entry 3n1a
(Hsieh et al., 2010), the cyclo-(L-His-L-Pro) molecule (CHQ A1514) 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 Asp143 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 B501) 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). The 2.0 Å resolution mFo − DFc maps contoured at ±3σ (green/red) and 2mFo − DFc maximum-likelihood omit maps contoured at 1σ (blue) are shown. Maps were calculated for a refined model with the ligand atoms omitted.