Hi
I'm not sure if anyone has mentioned this yet, but if you use
"hklview" to view the mtz file (assuming you're working in ccp4-
land), you can probably get a better handle on the systematic
absences than by looking at the original images.
I'm told there are other tools available to examine your reflection
file graphically, but I haven't used them so I can't comment on them.
On 1 Dec 2010, at 17:58, Phoebe Rice wrote:
> Its may be an interesting question of pseudosymmetry. The best
> thing would be to find a local mentor who could have a good hands-
> on look, but here are some thoughts:
>
>> From the space group tables you will see that P212121 has half as
>> many asymmetric units as C2221, and C2221 has crystallographic
>> twofold axes that your dimer could lie on. So both space groups
>> are perfectly consistent with the protein being a dimer. (You
>> must be able to see the symmetric dimer when you rebuild your
>> model in C2221 during the refinement process?)
> The R-factor might be higher in P212121 because you're refining two
> molecules instead of one, and thus there are more degrees of
> freedom. If the space group does turn out to be P212121, you
> should probably find a local expert for detailed refinement advice.
>
> The centering in C2221 should give a different pattern of
> systematically missing spots, so you should have a carefull look at
> the original images and the output of the scaling in C2221, and see
> if the additional missing spots are really missing or not. (Don't
> forget the axes may be permuted between the two indexing systems).
> If they're present but weak, its P212121. In that case, you should
> note that the systematically weak spots will distort the standard
> twinning statistics.
>
> Hope that helps!
> Phoebe
>
> =====================================
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/
> 01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
>
> ---- Original message ----
>> Date: Wed, 1 Dec 2010 16:17:58 +0800
>> From: CCP4 bulletin board <[log in to unmask]> (on behalf of
>> Xiaopeng Hu <[log in to unmask]>)
>> Subject: [ccp4bb] Space group and R/Rfree value
>> To: [log in to unmask]
>>
>> Dear all,
>>
>> I am working on a data-set (2.3A) and the space group problem
>> bothers me a lot.The space group of the data-set could be C2221 or
>> P212121, since our protein functions as a dimer, and P212121 gives
>> two molecular in the asym-uint, I think P212121 is more reasonable
>> than C2221.However with C2221, I can refine the R/Rfree to 20/24
>> or lower, while with P212121 only to 26/30. Also Phenix points out
>> that the crystal is probably a twin with P212121 but is OK with
>> C2221.
>>
>> I am not a real crystallographer, perhaps this problem is stupid,
>> any help will be appreciated!!
>>
>> Best wishes,
>>
>>
>> Xiaopeng Hu
Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH
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