<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
</head>
<body ocsi="0" fpstyle="1">
Dear Bret,<br>
<br>
I'd bet your structure is pseudo-merohedrally twinned in P21 (twinning operator h,-k, -l).
<br>
We had a similar problem with gp26 structure (an elongated fiber) that crystallized in a<br>
pseudo-P212121 cell, which, in reality was P21 with dimensions<br>
a = 40.5 b = 117.5 c =171.6 Å with the β-angle ~90.2° <br>
Refinement was stuck at ~32% before taking into account twinning.<br>
Good luck!<br>
<br>
Gino<br>
<br>
<br>
<br>
<br>
******************************************************************************<br>
Gino Cingolani, Ph.D.<br>
Associate Professor<br>
Thomas Jefferson University<br>
Dept. of Biochemistry & Molecular Biology<br>
233 South 10th Street - Room 826<br>
Philadelphia PA 19107<br>
Office (215) 503 4573<br>
Lab (215) 503 4595<br>
Fax (215) 923 2117<br>
E-mail: gino.cingolani@jefferson.edu<br>
Website: http://www.cingolanilab.org<br>
******************************************************************************<br>
<br>
"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"<br>
<br>
("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
From: phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Bret Wallace [bretw319@gmail.com]<br>
<br>
Sent: Sunday, March 18, 2012 11:37 AM<br>
<br>
To: phenixbb@phenix-online.org<br>
<br>
Subject: [phenixbb] Refinement using data with pseudo translational symmetry<br>
<br>
<br>
<br>
<br>
<br>
To all,<br>
<br>
<br>
<br>
First I apologize for the long email, but I wont to make sure that I give enough information to describe the problem.<br>
<br>
<br>
<br>
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<br>
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<br>
(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.
<br>
Here are the details for the data/structure:<br>
<br>
<br>
<br>
SG: P212121<br>
<br>
Cell: 72 124 175 90 90 90<br>
<br>
Res: 50-2.8<br>
<br>
<br>
<br>
<br>
<br>
Patterson analyses<br>
<br>
------------------<br>
<br>
<br>
<br>
Largest Patterson peak with length larger than 15 Angstrom <br>
<br>
<br>
<br>
Frac. coord. : 0.155 0.000 0.500<br>
<br>
Distance to origin : 87.222<br>
<br>
Height (origin=100) : 34.517<br>
<br>
p_value(height) : 6.739e-04<br>
<br>
<br>
<br>
<br>
<br>
The reported p_value has the following meaning:<br>
<br>
The probability that a peak of the specified height<br>
<br>
or larger is found in a Patterson function of a<br>
<br>
macro molecule that does not have any translational<br>
<br>
pseudo symmetry is equal to 6.739e-04.<br>
<br>
p_values smaller than 0.05 might indicate<br>
<br>
weak translational pseudo symmetry, or the self vector of<br>
<br>
a large anomalous scatterer such as Hg, whereas values<br>
<br>
smaller than 1e-3 are a very strong indication for<br>
<br>
the presence of translational pseudo symmetry.<br>
<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
I should also not there is no twinning detected by either xtriage or twinning servers.<br>
<br>
<br>
<br>
I have done a number of things to try to resolve this:<br>
<br>
<br>
<br>
-rescaling in lower symmetry (P21 and P1)<br>
<br>
-rescaling in the PG P222 and letting the MR program decide the proper space group<br>
<br>
-shifting origin and re-refining<br>
<br>
-a number of different refinement protocols (TLS, optimized weights/adp, simulated annealing, several cycles of rigid body, etc.)<br>
<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
Does any know of any other possible things I should try to refine this data? I am happy to provide additional information upon request.<br>
<br>
<br>
<br>
Thanks in advance for any help!<br>
<br>
Bret<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</body>
</html>