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
