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
