Dear Fatima, just a couple of things you may consider: - you can let shelxl refine the occupancy by assigning a free variable to the whole ligand - did you refine the structure anisotropically? At this resolution you certainly should. - maybe you made a mistake converting the files from refmac to shelxl, e.g. you might have used amplitudes where shelxl expects intensities or vice versa.
Good luck, Tim On Mon, Jun 07, 2010 at 05:46:01PM +0100, Fatima Fonseca wrote: > 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 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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