Absent ligand density in the omit map. In the structure of the Nudix hydrolase DR1025 from Deinococcus radiodurans, PDB entry 1sz3
(Ranatunga et al., 2004), the nonhydrolyzable GDP analogue (GNP 3030A) is placed in a conformation and position entirely unsubstantiated by 2mFo − DFc electron density. The 1.6 Å resolution mFo − DFc map contoured at ±3σ (green/red) and 2mFo − DFc maximum-likelihood omit map contoured at 1σ (blue) are shown. Maps were calculated for a refined model with the ligand atoms omitted.