[phenixbb] Refinement using data with pseudo translational symmetry

Gino Cingolani Gino.Cingolani at jefferson.edu
Sun Mar 18 08:52:47 PDT 2012

Dear Bret,

I'd bet your structure is pseudo-merohedrally twinned in P21 (twinning operator h,-k, -l).
We had a similar problem with gp26 structure (an elongated fiber) that crystallized in a
pseudo-P212121 cell, which, in reality was P21 with dimensions
a = 40.5 b = 117.5 c =171.6 Å with the β-angle ~90.2°
Refinement was stuck at ~32% before taking into account twinning.
Good luck!


Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab (215) 503 4595
Fax (215) 923 2117
E-mail: gino.cingolani at jefferson.edu
Website: http://www.cingolanilab.org

"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"

("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Bret Wallace [bretw319 at gmail.com]

Sent: Sunday, March 18, 2012 11:37 AM

To: phenixbb at phenix-online.org

Subject: [phenixbb] Refinement using data with pseudo translational symmetry

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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