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
