[phenixbb] Trouble refining following molecular replacement

Tyler Liban tliban at ucsc.edu
Tue Dec 22 10:49:36 PST 2015

Hello all,

We are currently working with a dataset for a trimeric protein complex at
3A that is giving us some issues.  The space group seems to be P21 ( 59.5,
61.6, 99.6 , 90, 98, 90) and the Mathews coefficient (2.6) suggests 2
copies of this 35kDa complex in the ASU.  We are using a homolog as the
search model that is 80% identical, and Phaser is able to find 2 molecules
in P21 when searching in the same point group and gives good TFZ scores
(TFZ = 9 or 10).  However, these solutions do not refine well following
Phaser (Rfree ~.50), and after removing parts of the model that look
incorrect the Rfree still stays between .46 and .50.  We ran the data
through Xtraige and saw no signs of twinning based on the L-test, and the
Patterson map has one small off-origin peak that is only 5%, indicating
that there is no significant pseudotranslation.  We have also tried finding
MR solutions in P1, but haven’t had much luck.  Any ideas on where to go
from here would be greatly appreciated.

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