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Hi Bret,<br>
<br>
if you send me the model (the most current you have) and the data
then I will have a look.<br>
<br>
Did you try to let phenix.refine build and refine water? Given the
resolution and the fact that you did not add water the R-factors 28
and 33 seem reasonable (to me).<br>
<br>
Pavel<br>
<br>
On 3/18/12 8:37 AM, Bret Wallace wrote:
<blockquote
cite="mid:CA+eJyhgQzDGhh6+Av7LUO8dgF8_cLxoSLD-86eMfqB9b=CG4DQ@mail.gmail.com"
type="cite">To all,<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>
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:<br>
<br>
SG: P212121<br>
Cell: 72 124 175 90 90 90<br>
Res: 50-2.8<br>
<br>
<br>
Patterson analyses<br>
------------------<br>
<br>
Largest Patterson peak with length larger than 15 Angstrom <br>
<br>
Frac. coord. : 0.155 0.000 0.500<br>
Distance to origin : 87.222<br>
Height (origin=100) : 34.517<br>
p_value(height) : 6.739e-04<br>
<br>
<br>
The reported p_value has the following meaning:<br>
The probability that a peak of the specified height<br>
or larger is found in a Patterson function of a<br>
macro molecule that does not have any translational<br>
pseudo symmetry is equal to 6.739e-04.<br>
p_values smaller than 0.05 might indicate<br>
weak translational pseudo symmetry, or the self vector of<br>
a large anomalous scatterer such as Hg, whereas values<br>
smaller than 1e-3 are a very strong indication for<br>
the presence of translational pseudo symmetry.<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>
I should also not there is no twinning detected by either xtriage
or twinning servers.<br>
<br>
I have done a number of things to try to resolve this:<br>
<br>
-rescaling in lower symmetry (P21 and P1)<br>
-rescaling in the PG P222 and letting the MR program decide the
proper space group<br>
-shifting origin and re-refining<br>
-a number of different refinement protocols (TLS, optimized
weights/adp, simulated annealing, several cycles of rigid body,
etc.)<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>
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>
Thanks in advance for any help!<br>
Bret<br>
<br>
<br>
<br>
<br>
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<br>
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</blockquote>
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