C222 means 2 possible space groups C222 and C2221. P222 means 8 possible space groups.
ps: I don't understand the C2221A and C222A listed by phaser when I chose the "alternative space groups (listed)" option in C222 space group, because when I chose "all alternative space group", only C222 and C2221 were test, not C2221A and C222A. 2012/8/3 Roger Rowlett <rrowl...@colgate.edu> > 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: rrowl...@colgate.edu > > 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 > > >
