Polder maps: improving OMIT maps by excluding bulk solvent

Abstract

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available in PHENIX.

Keywords: OMIT maps; PHENIX; bulk solvent; ligand validation; polder maps; residual (difference) Fourier synthesis; weak density.

Figure 1

Illustration of how the bulk-solvent mask changes when a ligand (MES 88, PDB entry 1aba) is included (a) or excluded (b) in its construction. Exclusion of the ligand results in the bulk solvent filling the area previously occupied by the MES molecule.

Figure 2

(a) A ligand molecule (GRG, PDB entry 4opi) is moved to an arbitrary location in the bulk-solvent region devoid of any electron-density peaks that could justify its position. The volume around the ligand is excluded from mask calculation and its contribution to the structure factor is ignored. The mF _obs − DF _model map contoured at 3σ shows strong positive density that follows the shape of the molecule. (b) Example of the mask when ligand is taken into account for mask computation but not for structure-factor calculation (biased map). The protein region is marked 0 and the bulk-solvent mask is marked 1. The mask employed in (b) was used to compute the difference map in (a).

Figure 3

Working chart for phenix.polder. See text for details.

Figure 4

(a) OMIT map and (b) polder map for ligand GRG 502 in PDB entry 4opi. The positive and negative mF _obs − DF _model OMIT difference density contoured at 3σ is displayed in green and red, respectively. (c) OMIT map contoured at ±1.5σ, at which the ligand density has a similar shape to the polder map.

Figure 5

OMIT maps for ligand MES 88 in PDB entry 1aba. The positive and negative mF _obs − DF _model OMIT difference density is displayed in green and red, respectively. (a) OMIT map contoured at ±3σ. (b) Polder map contoured at ±3σ. (c) OMIT map contoured at ±2σ. (d) OMIT map using a Babinet solvent model (±3σ). (e) OMIT map not using any bulk-solvent model and truncating the data at 5 Å resolution (±3σ). (f) OMIT map using a Babinet model (±2σ). (g) OMIT map not using a solvent model and truncating at 5 Å resolution (±2σ).

Figure 6

(a) OMIT map and (b) polder map for ligand ABI 246 in PDB entry 1c2k. The positive and negative mF _obs − DF _model OMIT difference density contoured at 3σ is displayed in green and red, respectively. (c) OMIT map contoured at ±2σ, at which the ligand density has a similar shape as the polder map. The gray sphere represents a Zn ion.

Figure 7

(a) Original 2mF _obs − DF _model (blue, 1σ contour) and mF _obs − DF _model maps, (b) OMIT map and (c) polder map for residue GlnH105 in structure 1f8t. The positive and negative mF _obs − DF _model difference density contoured at 3σ is displayed in green and red, respectively. In (c), the Gln side chain was real-space refined in Coot.

Figure 8

R factor versus resolution for PDB entry 1aba computed using the flat bulk-solvent model (red squares), Babinet solvent model (green circles) and no solvent model at all (blue triangles).

Figure 9

Trial polder maps of ligand molecule ABI 246 in PDB entry 1c2k used for the computation of correlation coefficients as described in §5: m1 (a), m2 (b) and m3 (c). All maps are contoured at 2.5σ.

Figure 10

(a) Simulated-annealing OMIT map and (b) polder map for ligand GRG 502 in PDB entry 4opi. The positive and negative mF _obs − DF _model OMIT difference density contoured at 3σ is displayed in green and red, respectively.