Dear Stefan,
clearly a 3.4 potentially 3.3A dataset. Rmerge is just high because of
your multiplicity.
As long as Rpim (all) stays well below 50% you are fine.
Stunning you have identical values between "all" vs "within". This is
usually not the case.
bye,
Matthias
-----------------------------------------
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Phone (+44) 1865 287549;
Fax (+44) 1865 287547
Email [email protected]
Website http://www.strubi.ox.ac.uk
-----------------------------------------
On 7/22/2013 6:19 PM, Stefan Gajewski wrote:
Hey!
I was reading a lot lately on data processing and the ongoing debate
in the community on how to submit "Table 1".
Here is an example of medium resolution data integrated with XDS,
merged in SCALA and preliminarily refined in phenix.
Overall InnerShell OuterShell
Low resolution limit 49.06 49.06 3.58
High resolution limit 3.40 10.74 3.40
Rmerge 0.224 0.050 1.324
Rmerge in top intensity bin 0.049 - -
Rmeas (within I+/I-) 0.235 0.052 1.391
Rmeas (all I+ & I-) 0.235 0.052 1.391
Rpim (within I+/I-) 0.067 0.014 0.407
Rpim (all I+ & I-) 0.067 0.014 0.407
Fractional partial bias 0.000 0.000 0.000
Total number of observations 275312 8491 39783
Total number unique 21137 765 3016
Mean((I)/sd(I)) 10.2 31.2 2.3
Completeness 98.4 95.7 98.4
Multiplicity 13.0 11.1 13.2
r_work=0.2461 (0.3998) r_free= 0.2697 (0.3592)
SigmaA highest shell = 0.78
scale factor highest shell (phenix.refine) = 0.87
Overall InnerShell OuterShell
Low resolution limit 49.59 49.59 3.80
High resolution limit 3.60 11.39 3.60
Rmerge 0.231 0.048 0.819
Rmerge in top intensity bin 0.045 - -
Rmeas (within I+/I-) 0.242 0.050 0.860
Rmeas (all I+ & I-) 0.242 0.050 0.860
Rpim (within I+/I-) 0.069 0.014 0.249
Rpim (all I+ & I-) 0.069 0.014 0.249
Fractional partial bias 0.000 0.000 0.000
Total number of observations 230945 6997 33402
Total number unique 17794 646 2531
Mean((I)/sd(I)) 11.5 30.7 3.7
Completeness 98.3 95.5 98.7
Multiplicity 13.0 10.8 13.2
r_work= 0.2372 (0.3585) r_free= 0.2663 (0.3770)
SigmaA highest shell = 0.79
scale factor highest shell (phenix.refine) = 0.95
XSCALE gives significantly lower average Rrim and Rmerge for both
integrations (~18%) and CC(1/2) is above 0.7 in all bins
The diffraction pattern looks great, the 3.4A reflections are visible
by eye and the edge of the detector is about 2.8A. The crystals were
10x20x50 um in size and spacegroup is P6522.
The maps shows signs of over fitting, the B-factors do not look
correct in my opinion. Note that the R-free value in the 3.4A shell is
lower than the R-work (and also the Rpim in that shell!) which clearly
indicates this refinement was not stable.
The structure contains no beta sheets and refinement also profits
greatly from very rigid high-order NCS. The maps are very detailed, in
fact better than some 2.8A maps I've seen before. The 0.2A in
question here are actually quite helpful to increase the map quality,
so I keep wondering if I should deposit the structure with them or
keep them only for my own interpretation.
Before I continue optimizing the integration/refinement I would like
to hear suggestions from the experts where to make the resolution
cut-off in this case?
Do I have all information I need to make that decision?
What arguments should I present when dealing with the reviewers? I
mean, the Rrim/Rmerge values are really very high.
Thank you for your input,
Stefan Gajewski
