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Figure 1
Most ligands in the PDB are modelled at unitary occupancy, and many partial occupancy ligands are not modelled with an alternate state. A histogram is shown of all ligand occupancies in the PDB classified by the presence of an alternate-conformer identifier (red, no conformer ID; blue, modelled with a conformer ID). Sub-unitary occupancy ligands are shown in the inset graph. Only the first instance of each ligand type from each PDB structure was used; following this all ligands with fewer than five non-H atoms or more than 50 instances were removed to avoid bias towards common molecules. Where alternate conformations of ligands are present, the total occupancy is used. The large majority of ligands are modelled in a single conformation at unitary occupancy (32 396, 92.1%). A smaller number have non-unitary occupancies but no alternate conformer identifier (1640, 4.7%). The remainder are modelled using alternate conformers (1122, 3.2%), of which 548 are ligands with alternate conformers that sum to unitary occupancy. Worryingly, there are also ten instances with more than 100% occupancy. These modelling statistics are unlikely to represent the true situation in crystal structures; ligands will always have a superposed solvent model when present at partial occupancy. The relationship between data-set resolution and the occupancy of partial occupancy ligands is shown in Supplementary Fig. S1; there is no clear trend towards occupancy refinement at high occupancy.

Journal logoSTRUCTURAL
ISSN: 2059-7983
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