I wonder if this could have happened here? Some one in the lab has yet again been trapped by a "feature??" of REFMAC. Say your MR solution is found to be in P21212 after you searched various orthorhombic SFs, but the input MTZ file has the space group still listed as P222 (i.e. the point group) then REFMAC will treat the solution as in P222, and NOT use the SG given on the PDB CRYST1 card.. You need to change the space group in the mtz header using one of the reflection utilities. CAD or SFTOOLS or REINDEX (without any reindexing..) all will rewrite the mtz file with the correct space group.
It would be nice if REFMAC reported any discrepancy in SG assignment as a fatal error.. Eleanor On 22 Jun 2012, at 00:53, Valerie Pye wrote: > Hi Sonali, > > You could try wide-search MR: > https://portal.sbgrid.org/d/apps/wsmr/ > > Best of luck, > > val > > On 20 June 2012 19:13, sonali dhindwal <sonali11dhind...@yahoo.co.in> wrote: > Dear All, > > I am working on a protein for last so many years and for which i have got > crystal now in a tray which i kept 1 years ago. It diffracts well and > resolution is 2.2A, which is good. > > I indexed in HKL2000, mosflm and automar and it shows P21 space group in all > data reduction packages. But when I tried using molrep or phaser then I do > not get any solution. The sequence of my protein is having 46% identity with > other available crystal structure. > Also when I tried to get matthews coffecient, it calculates its molecular > mass less ( about 35 kDa) than which should be (original 54kDa) with solvent > content 47%. > > I have also run the silver staining gel of the protein which contained > crystal that shows about 45 kD protein band which is 10 less than the > original. Also I tried to run gel on crystal but it did not give anything as > it was a small crystal. > > I have tried all combinations of the search model and tried to break > available pdb many ways to make different search models but have not got any > good solution. Molrep gives contrast even 10 or more but no good electron > density map yet. Free R and figure of merit becomes 52% and 42% respectively > in Refmac with all the solutions. > > I will highly appreciate all the suggestions for this kind of problem. > > Thanks and regards > > -- > Sonali >
