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 <CCP4BB@JISCMAIL.AC.UK> (on behalf of
Xiaopeng Hu <huxp...@mail.sysu.edu.cn>)
Subject: [ccp4bb] Space group and R/Rfree value
To: CCP4BB@JISCMAIL.AC.UK
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
