Hello, My protein is 26 kDa and the resolution of the data is 1.90 angs. My ligand is 174 Daltons. and it was soaked into the crystal. Ligand is colored and the crystal after soaking takes up intense color. However if we soak more than optimum, the color deepens in intensity but the crystal diffracts no more. So perhaps the ligand's occupancy can not be the 1.00.
After model building I see ligand density, starting to appear at 0.7 sigma and clear at 0.5-0.6 sigma, close to the protein residue where it "should" bind. Occupancy is ~0.6 after the refinement and B factors for the atoms of the ligand range from 30-80. Questions I have (1) What is the acceptable sigma level for very small ligands for peer review/publication? (2) I did refinement by Refmac and by Phenix refine, separately. The map quality for the ligand is better after the refmac refinement than after the Phenix refinement. Why is such a difference and which one should I trust? I used "mostly" default parameters for both (Phenix and Refmac) before the refinement. Thanks for your time. Amit
