 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 3]](lv5055fig3mag.jpg)
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Figure 3
Examples of problematic structures in the Iridium test set. Electron density after the first round of refinement (prior to ligand fitting) is displayed as a gray mesh for the 2mFo − DFc map (contoured at 1.0σ) and as green and red meshes for the mFo − DFc map (contoured at ±3.0σ). The published model is shown as purple sticks. Yellow sticks represent the refined model at the end of pipeline execution; orange sticks represent incorrect or rejected ligand placements. (a) PDB entry 1oq5 . The ligand is correctly placed but is rejected because the CC to the mFo − DFc map falls below the default cutoff of 0.7. (b) PDB entry 1mq6 . The ligand is partially misfitted in the run with default settings (orange sticks) owing to ambiguous mFo − DFc density. Filtering the map with a maximum-entropy procedure results in correct placement (c). (d) Ligand placement in 1hp0 , showing deviation from the published structure. (e) Misfitted ligand in 1hp0 with calcium ion (purple sphere) removed from the starting model. |
![[Figure 3]](lv5055fig3.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
