Uhnsoo, Well you only have half of your 4-heterodimers, so your phases are poor, particularly for the missing 50% of your structure. DM and NCS averaging/solvent flattening will only work if the missing 50% can be properly masked. One possible out from this hole is to try RESOLVE. If you tell RESOLVE the solvent content then it will try to determine the appropriate protein mask from the ED. It will also apply NCS based on a selection of atoms, from your MR solution, in the file ha.pdb or provide the NCS matrices explicitly. This has worked for me in the past with a poor MR solution at low resolution (3.5 A), half of the molecule was in the incorrect orientation, but the DM modified ED showed the correct orientation quite clearly. The 70% solvent content really helped in this case.
Good Luck, Mark On Wed, 2007-02-21 at 12:30 -0800, [EMAIL PROTECTED] wrote: > Dear all, > > Recently, I've gotten a 3.1A data set with a P1 space group. Based on a > Mattchew > coefficient, I have 4 hetero-dimer molecules in one asymmetric unit. Because > one > of the dimers was known already, I tried MR with a program Phaser and molrep > (Amore doesn't calculate a translation function with a P1 space group). > Phaser gave > me a reasonable solution with Z-score closed to 20 and LL-gain over 900(molrep > didn't give me a good solution), and that solution has 4 molecules with quite > reasonable packing with local 2-fold symmetries. I also ran Phaser with > different wavelength ranges with different truncated forms, and always the > solutions were the same. However, when I calculated the map, the map was still > messy and I couldn't see a clear density of the other molecules. I also ran a > rigid body refinement and a restrained refinement with different programs > (refmac and cns), but the R factor didn't drop. I ran DM with ncs averaging > and > solvent flattening, still the map wasn't improved. At this moment, we are > still > sure that our data set has a P1 space group with good statistics and the > solution from phaser is quite reasonable. > > Is it possible that P1 space group can be a problem during MR? Do you think > the > solution from Phaser is just wrong or did I miss something? > > Any suggestions will be helpful to me. > > Thanks, > > > > > uhnsoo Sincerely yours, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Fax. (409) 747-4745 mailto://[EMAIL PROTECTED] http://xray.utmb.edu http://xray.utmb.edu/~white
