1. How does the MR map look like ? Do you see features resembling a real solution or just noise ?
2. If the map looks decent, then try running a rigid body refinement using Refmac. Does the Rwork/Rfree dro ? 3. At this point you should look at the difference density map in Coot and be able to identify "wrong" amino acids e.g. if your MR model had an Ala where there is truly a His or Phe, you should see a huge blob of green density indicating the missing atoms in your current model. 4. Fix the sequence of your MR model to your true sequence 5. WARNING don't continue to read the next option if you want to learn and have fun by yourself ! 6. at 1.9 Å ARP/wARP will be able to build most of your structure automatically Jürgen P.S. It's likely you have the correct space group simply by gaussian distribution over P222 pointgroups, but maybe that's what the Rwork/Rfree are indicating Did you run Phaser in P222 + all other possible space groups or did you feed it with P212121 and only ran it in this space group ? - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Oct 18, 2010, at 7:39 PM, Jyotica Batra wrote: > Hi All > > I have a dataset at 1.9A, spacegroup-P212121 (unit cell: 37.7, 39.52, 231.72, > 90, 90, 90), > I used MR phaser and got a structure solution with LLG= 320 (1copy/a.u) . > During refinement, the R-free (50%) and R-factors (42%) never go down. > I have tried refining in phenix and refmac both, but still the high R-free > problem persists. At this point I'm seeking help to know the possible > reasons for this high R-free. > > Thanks in advance! > > Jyotica > >
