FIGURE 2.

Conventional OMIT maps do not generally produce clear unambiguous evidence of binding for low occupancy ligands, even at high resolution. Examples for four binding fragments showing different levels of support for binding from OMIT maps, where clear evidence of binding is shown by PanDDA event maps. Map coloring: 2mF_o-DF_c maps are shown as blue mesh and all difference maps are shown as green/red mesh; associated PanDDA event maps are shown as purple surfaces. Map type and contour are as indicated. Both types of OMIT maps are produced by phenix.polder. Maps are truncated (carved) at 3Å around relevant residues and ligands for clarity; PanDDA maps are carved at 2Å. Model coloring: To distinguish alternate conformations, carbon atoms for ligand-associated conformations are coloured orange and non-ligand-associated conformations are coloured blue; main-conformation (full-occupancy) atoms are coloured light gray; all other atoms are colored by element except waters, which are coloured as per carbon atoms. Resolutions: (A) 1.40Å, (B) 1.60Å, (C) 1.29Å, (D) 1.34Å. Refined ligand occupancies: (A) 0.41, (B) 0.50, (C) 0.38, (D) 0.22. PanDDA event map pseudo-occupancies (1-BDC): (A) 0.15, (B) 0.17, (C) 0.10, (D) 0.11. (A) Binding is not evident in the 2mF_o-DF_c maps at a moderate contour level, but is clearly supported by both types of OMIT map, especially when considered in combination with the extra density from the superposed water molecules from non-ligand-associated conformations, as modeled. It is debatable whether the OMIT maps alone would provide strong enough evidence to support modeling of the ligand, but the single ligand conformation is clearly evidenced in the PanDDA event map, preventing potential misinterpretation of the OMIT map as multiple conformations of the ligand. (B) Similar to (A), but with less evidence in the simple OMIT map. The polder OMIT map provides an envelope which fits well with the envelope provided by the ligand and the superposed water molecules, as modeled. It is unlikely either OMIT map would be accepted as evidence of binding, but once more, the ligand conformation is clearly identified in the event map. (C) OMIT maps show mostly features which correspond to superposed (not-ligand-associated) waters, and do not present evidence for the bound ligand, unlike the event map. (D) Ligand binding coincides with an alternate conformation of an arginine residue, which dominates the refined maps and OMIT maps.