It is not clear to me why you believe that cutting the resolution of the data would improve your model (which after all is the aim of refinement). At the edge CC(1/2) and I/sigI are perfectly respectable, and there doesn’t seem to be anything wrong with the Wilson plot. Th R-factor will of course be higher if you include more weak data, but minimising R is _not_ the aim of refinement. You should keep all the data
I don’t know what xtriage means by “large number of outliers”: perhaps someone else can explain
Phil
> On 29 Mar 2017, at 14:54, Juliana Ferreira de Oliveira <[log in to unmask]> wrote:
>
> Hello,
> I have one dataset at 2.3 Å (probably it can be better, I/σ = 2.1 and CC1/2 = 0.779, the summary data is below), but when I perform Xtriage analysis it says that “There are a large number of outliers in the data”. The space group is P212121. When I refine the MR solution the Rfree stops around 30% and it doesn´t decrease (in fact if I continue refining it starts to increase).
> The Wilson plot graph is not fitting very well between 2.3 and 2.6 Å:
>
> <image001.jpg>
>
> So I decided to cut the data at 2.6A and Xtriage analysis doesn’t notify about outliers anymore. I could refine the MR solution very well, the final Rwork is 0.2427 and Rfree = 0.2730 and validation on Phenix results in a good structure.
> I run Zanuda to confirm the space group and it says that the space group assignment seems to be correct.
> Do you think that I can improve my structure and solve it at 2.3 Å or better? Or I can finish it with 2.6 Å? To publish at 2.6 Å I need to justify the resolution cut, right? What should I say?
> Thank you for your help!
> Regards,
> Juliana
>
> Summary data:
> Overall InnerShell OuterShell
> Low resolution limit 51.51 51.51 2.42
> High resolution limit 2.30 7.27 2.30
> Rmerge 0.147 0.054 0.487
> Rmerge in top intensity bin 0.080 - -
> Rmeas (within I+/I-) 0.155 0.057 0.516
> Rmeas (all I+ & I-) 0.155 0.057 0.516
> Rpim (within I+/I-) 0.048 0.017 0.164
> Rpim (all I+ & I-) 0.048 0.017 0.164
> Fractional partial bias -0.006 -0.003 0.146
> Total number of observations 83988 2907 11885
> Total number unique 8145 307 1167
> Mean((I)/sd(I)) 9.3 23.9 2.1
> Mn(I) half-set correlation CC(1/2) 0.991 0.998 0.779
> Completeness 99.9 99.5 100.0
> Multiplicity 10.3 9.5 10.2
>
> Average unit cell: 37.57 51.51 88.75 90.00 90.00 90.00
> Space group: P212121
> Average mosaicity: 1.90
>
>
> Juliana Ferreira de Oliveira
> Brazilian Laboratory of Biosciences - LNBio
> Brazilian Center for Research in Energy and Materials - CNPEM
> Campinas-SP, Brazil
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