Dear All: I try to solve a structure by using Phaser.
The data set was collected at 3.9 A with 98.1% (95%) completeness. Based on pointless, the best space group for the data set is P21212. And the data can be processed with P21, P212121 as well. The I/sigma value for the data is 13.3 (1.9). There are some structure models available from PDB with space groups at P21, P212121 or P21212. I used these structures as templates to get initial models. I then use Refmac5 to refine the models. But the R-factors/R-free are around 0.5 /0.5. When I exam the .pdb and .mtz in coot, the models are not aligned with density. I then use the templates (PDB entries) against the processed .mtz files using Refmac5. Again, the R-factors are higher than 0.5. I notice that my data set has different cell units with templates. When the space group match to one template, the cell dimensions is differ from the template. When the cell dimension matches to one template, the space group is different. Is this the problem for modeling? Sequence identity between my protein and templates is 99%. Two residues were mutated in my protein. I use Phaser for molecular replacement, and Refmac5 for refinement. Data was processed using xds or mosfilm. Thank you for advice Uma On Wed, Aug 1, 2012 at 2:27 PM, Uma Ratu <rosiso2...@gmail.com> wrote: > Dear All: > > I try to use Phaser to solve the structure by Molecular Replacement. > > The data set is collected @180 degree. I process the data using HKL, and > have resonable good score: rejection (0.05), Linear R-factor (0.038), > completeness (98.3), resolution (50-1.5). > > I then use Phaser to do MR. The parameter setting are: > automated search > components in asymmetric unit; number of residue 1332; number in > asymmetric unit 1 > perform search search using "ensemble1" number of copies to search for 4 > > The protein is in tetramer form. I define this by using the residue number > (1332) which is 4 x monomer. > > After run, Phaser only gave 9 partial solutions, and no solution with all > components. The resulted PDB contains only dimer form of the protein, not > the tetramer. And the first TFZ score is around 2.5, which is too low for > MR. > > I have the report file of data processing and the summary of Phaser > attached. > > Could you please advice which part is wrong, why can I get the tetramer > form of the protein? > > Thank you > > Uma >
