Dear all, I solved the structure of an enzyme at resolution of 1.1A with a bound substrate using Refmac5 and Coot for refinement/building. I have a very nice density for my ligand and a very good structure, as judged by Molprobity analysis.
Now I'm using SHELXL to finish refinement but most of the density for my ligand disappears when I put it in, and it gets very high B factors. I though it could be some problem with the occupancy so I did a set of runs with different occupancies ranging from 0.2 to 1 and I got the best R factors when using 0.4/0.5 for the occupancy. However, I still have most of the ligand outside electron density… In Coot I get no ligand with “Find ligand” even when I reduce the cluster sigma level to 0.8. What am I missing here? Just another question, how to reduce the acceptable fit fraction in Coot “Find ligand”? Thanks for any advice, Fátima
