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Thank you very much for your comments. I re-do the data process with P21, and use the output for Phaser. This time, Phaser finishes with good resolution, the TFZ is 28. And the model is tetramer. Cheers Uma On Thu, Aug 2, 2012 at 9:45 PM, Roger Rowlett <[log in to unmask]> wrote: > A few thoughts: > > 1. Search for all possible space groups (e.g., P2 and P21 in this > case). Be happy it isn't C222, which means 8 possible combinations of screw > axes to search! As mentioned already, P21 is far more common than P2. I > think P21 is one of the most common space groups in protein crystallography. > 2. How are you determining how many copies of the search model go in > the ASU? It is not necessarily one biological unit, or an integral number > of biological units. Run a cell content analysis in Phaser (e.g. Matthews > probability calculator) and start there, but consider the results a > suggestion only. For larger ASUs, the predicted number is not very > accurate. "Six" might actually be 4 or 8 chains. > 3. Look at the crystal packing in Pymol, Coot, or in you favorite > tool. You can do this by enabling a large symmetry molecule radius. If you > see a regular lattice of proteins with nice solvent channels and > protein-protein contacts, things are looking up. (But you can be fooled > into a premature victory at times.) > 4. Partial Phaser solutions may provide a big hint about how many > molecules are in the ASU when packing is examined. Often the placement of > the missing molecules is quite obvious, as it completes a solvent channel > or fills in symmetrical protein-protein contacts. > 5. Finally, look at the maps. Crappy maps probably mean the wrong > space group, especially if chains don't pack well. Good maps with good > packing usually mean you are on the right track. > > Cheers and good luck, > > _______________________________________ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: [log in to unmask] > > On 8/1/2012 2:27 PM, Uma Ratu 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 > > >