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Dear Mohinder, What one should really do is to provide an accurate model (including the space group) of what is taking place in the crystal. For example, there was this case reported by Morales et al. (2000, Acta Cryst sect. D56, 1408-1412) of a complex of 2 proteins (i.e. identical situation to that of a complex between protein and small ligand); the apparent space group was P4(3)2(1)2, however the smaller protein was binding in 2 "opposite" orientations in the complex. This led to an arrangement of the smaller protein in an orthorhombic space group [P2(1)2(1)2(1)] and the structure had to be treated as a twin in order to give the "best" (most appropriate) model of what was taking place in the crystal. So I think it is important to carefully consider (and understand) what is going on, in order to do the most appropriate modeling. You could have an apparent orthorhombic space group, whereas the correct space group (dictated by the small molecule) is different. Fred. 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 >