Hi Chris,
I personally would go with your "thick" dataset. 90% completeness is
not stellar, but in my opinion not detrimental, either.
I had one project that persistently yielded crystals that diffracted
to rather high resolution (2.3), but in one direction no lunes were
discernible and - consistent with that - the other direction's
diffraction consisted of lines that had little beads on them - i.e.
extremely smeary spots. XDS was the only program to integrate this data
at an Rmerge better than 25% (it actually got below 10%).
I was able to phase this data experimentally (Fe-MAD), use NCS and end
up with amazing maps. Nevertheless, refinement was a bitch: It never
went significantly below 30 for Rfree and messed up the geometry of the
model, even though the electron density was clearly showing where the
model should be. My explanation for this was that this was a rare case
were the phases were actually determined better than the Fs. If you look
back, in the days before refinement, reflection intensities were not
measured, they were classified as weak, medium and strong - and that was
enough to generate meaningful electron densities.
In a cases like that, were the accurate determination of integrated
intensities is a a problem, there should be a mechanism to submit
experimental electron density instead of refined models, as the latter
will make way less sense.
So again - you got lucky with your "thick" dataset -- use it and don't
sweat the 90% completeness!
HTH,
Jens
On Fri, 2014-02-21 at 18:41 -0600, Chris Fage 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
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