I can't help but suggest to also try PDB_REDO for tuning refinement.
http://xtal.nki.nl/PDB_REDO/index.jsp
One of the things you get, is exactly what Pavel explains below, how your
structure looks in comparison with others in similar resolution, but also with
the PDB_REDO data bank structures.
I will also agree that the 90% complete data set might be best - just refine
both models, compare, and choose the best one according to validation criteria
(you get a few for free in PDB_REDO and of course in eg Molprobity)
Tassos
Sent from my iPad
On 22 Feb 2014, at 02:20, Pavel Afonine pafon...@gmail.com wrote:
Chris,
what you get is not unheard of but clearly you are not in majority: at around
1.95A resolution distribution of R-factors in PDB is:
Histogram of Rwork for models in PDB at resolution 1.85-2.05 A:
0.093 - 0.118 : 3
0.118 - 0.143 : 75
0.143 - 0.168 : 821
0.168 - 0.193 : 2617
0.193 - 0.218 : 2950
0.218 - 0.242 : 1147
0.242 - 0.267 : 201 your case
0.267 - 0.292 : 21
0.292 - 0.317 : 2
0.317 - 0.342 : 1
Histogram of Rfree for models in PDB at resolution 1.85-2.05 A:
0.138 - 0.160 : 12
0.160 - 0.183 : 106
0.183 - 0.205 : 742
0.205 - 0.227 : 1971
0.227 - 0.249 : 2566
0.249 - 0.272 : 1676
0.272 - 0.294 : 616
0.294 - 0.316 : 119your case
0.316 - 0.339 : 24
0.339 - 0.361 : 6
Histogram of Rfree-Rwork for all model in PDB at resolution 1.85-2.05 A:
0.001 - 0.011 : 67
0.011 - 0.021 : 428
0.021 - 0.031 : 1324
0.031 - 0.041 : 2220
0.041 - 0.050 : 1975
0.050 - 0.060 : 1059 your case
0.060 - 0.070 : 459
0.070 - 0.080 : 201
0.080 - 0.090 : 75
0.090 - 0.100 : 30
Pavel
P.S.: Command to the statistics as above is:
phenix.r_factor_statistics 1.95
On Fri, Feb 21, 2014 at 4:41 PM, Chris Fage cdf...@gmail.com wrote:
Dear CCP4BB Users,
I recently collected a number of datasets from plate-shaped crystals
that diffracted to 1.9-2.0 angstroms and yielded very nice electron
density maps. There is no major density unaccounted for by the model;
however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
~0.30, respectively. Probably due to the more 2-dimensional nature of
my crystals, there is a range of phi angles in which the reflections
are smeared, and I am wondering if the problem lies therein.
I would be grateful if anyone could provide advice for improving my
refinement statistics, as I was under the impression that the
R-factors should be ~5% lower for the given resolution.
A few more pieces of information:
-Space group = P21, with 2 monomers per asymmetric unit;
-Chi square = 1.0-1.5;
-Rmerge = 0.10-0.15;
-Data were processed in HKL2000 and refined in Refmac5 and/or phenix.refine;
-PHENIX Xtriage does not detect twinning, but hints at possible weak
translational pseudosymmetry;
-I was previously able to grow one atypically thick crystal which
diffracted to 1.65 angstroms with Rwork/Rfree at 0.18/0.22.
Unfortunately, the completeness of the dataset was only ~90%.
Regards,
Chris
