Dear Yurong,
your approach to individually refine each potential solution is correct. I do
not know how things are implemented in phenix.refine, but the first thing to
check is that your are using the correct space group as obtained from the MR
program. Some refinement programs use the space group from the reflection file
(MTZ), which may be the space group used for the processing instead of the
space group from the pdb file found by the MR program.
>From what you write, you must have non-crystallographic translations of almost
>0.5 in x and z direction. This means that you will have along these axis
>either exact 21 symmetry, where the ~0.5 shift will generate a pseudo 2-fold,
>or you have exact 2-fold symmetry where the pseudo symmetry will produce a
>pseudo 21 axis. With your low resolution data, this explains why you get
>solutions in all these space groups. You really have to try all combinations
>of crystallographic and non-crystallographic symmetry.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Yurong Wen
Sent: Monday, December 03, 2012 12:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Pseudo translational symmetry Problem or Wrong
Spacegroup
Dear All,
Recently, I collected a dataset of a protein-DNA complex and indexed in
spacegroup P212121 to 3.4 Å. However, Phenix.Xtriage indicated the presence
of a very high pseudotranslational symmetry peak. I scaled the data in
spacegroup P222. When I used the protein heterotetramer as search model to do
the MR, solutions are suggested in P22121, P212121, P2212, P21212 and all with
a TFZ score higher than 15, LLG higher than 570. Then I used phenix.refine to
refine those solutions; however the Rfree is as high as 0.54-0.56. The
refinement strategy that I used for the refinement is rigid body, group
B-factors and XYZ coordinates.
How to deal with this pseudotranslational symmetry problem? Does a
solution with such high TFZ scores mean that the correct one has been found?
How to solve the spacegroup problem in such situation?
Do you have any suggestions?
Thank you very much.
Greetings,
Yurong
