Hi all, Picture attached.
I solved the structure of a membrane protein using LCP. When trying to identify the cation-binding site, I co-crystallized with Rb+. I see strong density corresponding to Rb+, and it was confirmed in an isomorphous difference map. One problem: in the native structure I see strong density for a lipid molecule from the LCP, in which I can model in very well. In the Rb+ structure, I see more of a blob of density at low rmsd, but when at higher the spherical Rb begins to show. Based on the isomorphous differnece map showing nice spherical denstiy for Rb+, it seems the crystal I shot contains protein molecules with the lipid and others with Rb+. I currently have Rb+ modeled in, but there is lots of extra density surrounding it, corresponding to the lipid molecule. Should I put both molecules in the structure, even though it doesn't make much sense and would results in odd lipid-cation clashes? Or should I just leave the Rb+ without lipid since this makes sense chemistry-wise? Thanks, Jarrod ------------------------------------- Jarrod J. Mousa, Ph.D. Bruner Laboratory Department of Chemistry University of Florida email: mo...@chem.ufl.edu
