Negative difference density. The difference density map from the EDS (a) shows negative density at the −3σ level (indicating absence of the model) for saccharide units 5–6 (HA3) in PDB entry 1loh
(Jedrzejas et al., 2002). Saccharide unit 4 of HA2 is present but is partly displaced from density owing to the incorrect placement of the subsequent units 5 and 6. Omit maps (b) provide no electron density consistent with placement of the two HA3 units. The 2.0 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.