[phenixbb] pseudo translational symmetry
youssef ben ammar
ybenammar at gmail.com
Mon Jun 22 21:44:44 PDT 2009
I recently solved the structure of a protein containing 395aa using phenix
autosol. After autoBuild I got about 65% of the sequence docked with 2
monomers in the ASU.
After several refinement cycles the map has been improved and I build
manually the remaining amino acids. But the problem is that R and Rfree
didn't decrease below 0.28 and 0.33 respectively. I tried with NCS
restraints, TLS but without success.
When I revised phenix autosol logs carefully, I found that in xtriage the
analyses of the Patterson function reveals a significant off-origin peak
that is 41.59 % of the origin peak, indicating pseudo translational symmetry
and no twin laws were found.
The space group is P212121 (36.898, 59.45, 393.908, 90, 90, 90). The basic
statistics suggested 1 copy in the ASU (but the solution gave 2 copies per
ASU !!!). The same analysis done by ccp4i gave the same solvent content and
math. coef. in p21212 but with 2 copies per ASU.
In xtriage I found this suggestion: If the observed pseudo translationals
are crystallographic the following spacegroups and unit cells are possible:
space group P 21 21 2 (b-1/4,2*c,a) operator x, y+1/2, z
unit cell of reference setting (393.91, 36.90, 29.73, 90.00, 90.00, 90.00)
I am really stucked with the refinement and don't know how to deal with this
Any help or suggestions are welcome.
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