[phenixbb] Refinement using data with pseudo translational symmetry

Bret Wallace bretw319 at gmail.com
Sun Mar 18 08:37:58 PDT 2012

To all,

First I apologize for the long email, but I wont to make sure that I give
enough information to describe the problem.

I have been working on a structure of two proteins in complex with each
other (one forms a homodimer, with each monomer bound to 1 monomer of the
other protein), using data, that according to phenix.xtriage contains
pseudo translational symmetry (output pasted below).  I have done a lot of
searching of both the phenixBB and ccp4BB regarding solutions to this
problem, but unfortunately most responses seem to be directed at resolving
issues with MR. I have successfully performed MR using both phenix phaser,
ccp4 phaser (the most updated version), as well as molrep.  The issue
arises upon structure refinement, where my Rwork and Rfree are essentially
stuck at 28 and 33, respectively.  I have built the entire structure,
including ligands, except for any solvent molecules.  Here are the details
for the data/structure:

SG: P212121
Cell: 72 124 175 90 90 90
Res: 50-2.8

Patterson analyses

 Largest Patterson peak with length larger than 15 Angstrom

 Frac. coord.        :    0.155    0.000    0.500
 Distance to origin  :   87.222
 Height (origin=100) :   34.517
 p_value(height)     :    6.739e-04

   The reported p_value has the following meaning:
     The probability that a peak of the specified height
     or larger is found in a Patterson function of a
     macro molecule that does not have any translational
     pseudo symmetry is equal to  6.739e-04.
     p_values smaller than 0.05 might indicate
     weak translational pseudo symmetry, or the self vector of
     a large anomalous scatterer such as Hg, whereas values
     smaller than 1e-3 are a very strong indication for
     the presence of translational pseudo symmetry.

Xtriage notes that the if the PTS is crystallographic, that C2221 is a
possible SG (x+1/6, y, z+1/2).  However, neither XDS or HKL picks
orthorhombic C, and the indexing/integrating doesn't work if I force it.

I should also not there is no twinning detected by either xtriage or
twinning servers.

I have done a number of things to try to resolve this:

-rescaling in lower symmetry (P21 and P1)
-rescaling in the PG P222 and letting the MR program decide the proper
space group
-shifting origin and re-refining
-a number of different refinement protocols (TLS, optimized weights/adp,
simulated annealing, several cycles of rigid body, etc.)

I have used HKL2000 and XDS to index/integrate/scale the data, both yield
the same results, with slightly different completeness and Rmerge values,
but refining with either gives similar R factor values.

Does any know of any other possible things I should try to refine this
data? I am happy to provide additional information upon request.

Thanks in advance for any help!
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