[phenixbb] Refinement using data with pseudo translational symmetry
pafonine at lbl.gov
Sun Mar 18 08:53:27 PDT 2012
if you send me the model (the most current you have) and the data then I
will have a look.
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).
On 3/18/12 8:37 AM, Bret Wallace wrote:
> 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!
> phenixbb mailing list
> phenixbb at phenix-online.org
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