Dear Mohinder and Ed, If you process your data in a lower symmetry space group, you will have more unique reflections, since reflections which are related by the higher symmetry will be avaraged during scaling in a higher symmetry space group (i.e. a 2fold or 3fold axis), while in lower symmetry space groups they will not. So the observation to parameter ratio stays the same and is only depending on resolution and solvent content.
The question one has to ask of course is: are these reflections really different, or are they the same only not averaged? In the latter case, you have more reflections, but not more information. As Ed mentions, using tight "NCS" restraints would in this case mimick the crystallographic symmetry. I would calculate maps while leaving out the inhibitor (omit maps) and check that the inhibitor indeed has a unique conformation in the lower symmetry space group. In that case the symmetry of the inhibitor, and therefore of your crystal, is the lower symmetry. If the inhibitor has a twofold disorder in the lower symmetry space group, you really have a higher symmetry space group and should work with this space group. In that case you can fit a molecule on the twofold axis with an occupancy of 0.5 and Refmac will automatically recognize the special position. Best regards, Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Ed Pozharski Sent: Thursday, October 21, 2010 5:05 PM To: [email protected] Subject: Re: [ccp4bb] Regarding space group P1, P21 There is nothing fundamentally wrong with refining in P1 even if the P21212 symmetry is present. An effective way to reduce the number of parameters wold be to introduce tight restraints. If you decide to lower the symmetry, go with P21 as it still keeps your ligand off symmetry axes. You can then add tight ncs restraints for the protein part. Alternatively, you can finish up the refinement in P21212 but get the maps for your publication drawn in P21 (with appropriate explanation). The reason to use the highest symmetry possible is because it presumably gives you a more precise structure since data quality may be better in P21212. I am not quite sure what you mean by putting restraints on protein - NCS? If so, tight restraints should approximately reduce the number of effective parameters by the number of copies. It appears (perhaps someone will correct me) that *constraints* are only available in CNS, but tight restraints supposedly approach that limit. Ed. On Thu, 2010-10-21 at 13:05 +0100, 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 -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
