as others have said, there are many cases where the actual symmetry is 
lower than the apparent, because a small part of thesructure does not 
obey the higher symmetry. This seems to have happened to you - an 
inhibitor which has P21 symmetry in a structure with near P212121 symmetry..
In similar cases I found the pointless analysis very helpful. It gives 
you the CC for each symmetry operator seperately. If the P121 ones are 
marginally higher than the P2 1 1 then that isextra proof.
You need to integrate that data in P21 - the beta angle may not be 
exactly 90.

Eleanor


On 10/21/2010 04:31 PM, [log in to unmask] wrote:
> 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:[log in to unmask]] On Behalf Of Ed
> Pozharski
> Sent: Thursday, October 21, 2010 5:05 PM
> To: [log in to unmask]
> 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