Hello Anna
You've already found the correct number of molecules in the asymmetric
unit. 21% Rwork is a quite respectable value for a structure at this
resolution, and while 80% solvent is a relatively rare occurrence it's
not unprecedented (a couple of years back I did one at 3.0Å with 75%
solvent - PDB 4U6U). If you were missing half your asymmetric unit from
your model, Rwork would be held up in the mid-30% range and there would
be regions of relatively high difference density outside the model.
Phil Jeffrey
Princeton
On 7/11/17 12:31 PM, Koromyslova, Anna wrote:
> Dear CCP4 members,
>
> I am working on a structure of a protein in complex with an antibody
> fragment (approx. 50kDa together). Molecular replacement with closely
> related proteins always comes up with one complex in the asymmetric
> unit, although MW of protein to which Matthews applies is 125kDa and
> corresponds to two complexes.
>
> Phaser gives two warnings:
>
> Large non-origin Patterson peak indicates that translational NCS is present.
>
> Solutions with Z-scores greater than 27.2 (the threshold indicating a
> definite solution) were rejected for failing packing test
>
> I couldn’t get a solution with two subunits although I have tried
> multiple combinations including only conserved parts of both proteins
> and different space groups including P1. Phenix Autobuild also yielded
> only one complex.
>
> So, the question is whether I can use that structure as is despite very
> high solvent content (80%) or should I try smth else. I would be very
> grateful for any suggestions.
>
> When the solution with a single complex is refined the statistics are
> the following:
>
> R-work 0.2129
> R-free 0.2459
> Matthews Coefficient: 6.22
> Percentage Solvent: 80.22
> Resolution range (Å) 48.34 - 2.9 (2.98 - 2.9)
> Space group P 62 2 2
> Unit cell 167.45 167.45 143.538 90 90 120
> Multiplicity 19.1 (18.3)
> Completeness (%) 99.44 (94.39)
> Mean I/sigma(I) 24.59 (2.71)
> Wilson B-factor 64.28
> R-merge 0.1256 (1.186)
> R-meas 0.1291
> CC1/2 0.999 (0.85)
> CC* 1 (0.959)
>
> Thank you very much for your help,
>
> Anna
> Dr. Anna Koromyslova, Postdoctoral researcher
> German Cancer Research Center (DKFZ), F150
> Im Neuenheimer Feld 242
> D-69120 Heidelberg
> Germany
>
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