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
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