Hi Since you're using iMosflm to process the data, it is well worthwhile running the "Quickscale" task following integration (I would actually run it after integrating ~5 - 10 degrees of data) to see if the true crystal symmetry determined by analysing agreement of the intensities of symmetry related reflections is actually the same as that indicated by the penalties from indexing.
Remember that the relationship between the unit cell dimensions is a consequence of the true symmetry, not vice versa - most crystallographers who have been in the game more than a few years have examples of lower symmetry crystals with apparently higher symmetry cell dimensions - a relatively common occurrence to have cell dimensions that "look right" for tetragonal when the true symmetry is orthorhombic. Of course, following integration & scaling etc you would probably want to check for things like twinning etc... In general, I think you should probably solve and refine in the highest symmetry space group that is most consistent with your data. If the experiment gives you just as good results in the higher symmetry space group as the lower, I would go for the higher symmetry. In your case, if P21 solution/refinement is as good as P1, but both are better than P21212, I would tend towards using the P21 solution. On 21 Oct 2010, at 12:05, Mohinder Pal wrote: > Dear CCP4BB members, > > I have solved a protein-drug complex structure in P21212 space group. In > this structure, the drug molecule is falling on the two-fold symmetry axis > having averaged electron density with 0.5 occupancy. We tried a lot to > crystallize this protein-drug complex in different space group but no success > so far. I have tried to solve the same data in space group P1 (statistics > are fine as I have collected data for 360 degree). The map looks even better > with one conformation for a drug. Interestingly, then I reprocessed the same > data using imosflm in P21 space group which have penalty 1 compared to 4 for > P21212. The structure in P21 is also refining well (with one conformation > of the drug compound without symmetry axis at the ligand position). The > question is , is it a good practice to solve this structure in P1 and P21 > even if the data has higher symmetry? > > Secondly, I have been advised that I have to be careful to refine structure > in P1 as there will be problem regarding observation/parameter ratio if I add > too many water molecules. What will be the case if the electron density > present for water molecules? > > I can put restrains to protein structure but I am just curious to know one > restrain equals how many observations. > > I look forward to hear your suggestions. > > Kind regards, > > Mohinder Pal Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
