 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 3]](dz5074fig3mag.jpg)
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Figure 3
Examples of grid searches for the bulk-solvent parameters ksol and Rprobe with the shrink radius Rshrink set equal to Rprobe. For each selected pair of parameters, Bsol was determined by least-squares fitting of the bulk-solvent model plus macromolecular model structure factors to the observed diffraction data. The resulting Rfree values are shown as surface plots. The projection of the minimum of the surface onto the ksol, Bsol plane is indicated by a gray spot (except for in c). (a) p97/VCP–ADP (PDB code 1yqi ) at 4.25 Å resolution. (b) p97/VCP–ADP·AlFx at 4.4 Å resolution (PDB code 1yq0 ). (c) VCP–AMP-PNP at 3.5 Å resolution (PDB code 1ypw ). This structure is unusual as the distribution is fairly flat and the optimum is reached for Rprobe = 0. This behavior may be a consequence of the very weak and partially disordered electron density in the D2 domain for this crystal form. (d) For comparison with a high-resolution structure, the results are shown for the Sec5–Exo84 complex solved at 1.9 Å resolution (PDB code 1zc3 ; Jin et al., 2005  ), producing the expected values of ksol = 0.3 e− Å−3 and Rprobe = 1. |
![[Figure 3]](dz5074fig3.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
