Hi Thomas, MR of coiled coils can be quite tricky including considerations of being curved, etc. If conventional MR is failing (assuming you have tried different kinds of parameter and search model tweaks, you can also play around with the search thresholds in phaser), you may try the following:
If you have multiple copies in the asu, you may try to find the orientation of the NCS axis. If you think that the molecules may be aligned along a particular direction, you can then generate a list of rotation search angles manually in fine increments (couple of degrees) and then force a translation search around all these rotation angles and then follow it up with a packing function search. This is like a brute force rotation/translation search across all rotation angles. Therefore identification of the ncs axis/molecular orientation will provide some search time advantage. You can do this in PHASER. Check out the manual to run stand alone scripts for these steps. Although different from the above, the follg. reference may provide useful reading: Gonzalez L Jr, Brown RA, Richardson D, Alber T. Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism. Nat Struct Biol. 1996 Dec;3(12):1002-9. Also check tropomysin structure MR attempts from Carolyn Cohen's group. Regards, Debanu. -- Debanu Das, Structure Determination Core, Joint Center for Structural Genomics. Stanford Synchrotron Radiation Laboratory, Menlo Park, CA. -----Original Message----- From: CCP4 bulletin board on behalf of Thomas Edwards Sent: Fri 3/28/2008 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MolRep of coiled coils Dear BB, I am attempting molecular replacement with a 2.8A data set from crystals of a coiled coil of about 150 residues. Probably p21212 but maybe p2221. So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as judged by Z-scores, CCs, Rfactors, and whether there is any density outside the model (there should be - I'm using a slightly shorter model to search with). One possible problem is that the coiled coil may not be straight. It may have a slight curve to it. I have used models from the PDB that are straight or slightly curved, so far with no success. I have tried a few different resolution cutoffs too. I have tried single helix chains or dimeric coiled coils. Is there anything special about MR with coiled coils? Can anybody provide any tips/hints on MR with coiled coils?? Thanks Ed
