Hi Jarrod, I think these 5 helices are either slightly misplaced, or somewhat disordered. How does the main-chain density look like? Do you see a discrete main-chain, or is the main-chain blurred and does the helix look like a blurred cylinder? If the main-chain is clear, I would take off all side chains, run some refinement and look if you could recognize some side chains. They may have shifted a few residues from what you think they are based on the homology model. Another option is to take out the 5 helices and rerun MR with them, using the 7 good helices as a partial model. You could also take one helix out at a time and try to build them again from scratch. Finally, if these helices are somewhat disordered, nothing can be done except from trying to grow different crystals, e.g. by adding a (different) ligand. With 7 out of 12 helices well-defined, your structure will nevertheless be interesting.
Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jarrod Mousa Gesendet: Donnerstag, 27. März 2014 15:15 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Merging Data from Multiple Crystals Hi, I am trying to solve the structure of a membrane protein. The protein has 12 helices and I have a good molecular replacement model that seems to work for about half of the structure. I used chainsaw to convert the amino acid residues to that of my protein sequence, and the density fits the structure well on one side of the protein, but on the other side (about 5 helices), there doesn't seem to be any density for the side chains. Has anyone had experience with this? The completeness is high ~99% for 3.2 angstroms. The data was collected from fairly small crystals ~ 20um. Thanks.
