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 > <juliana.olive...@lnbio.cnpem.br> 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
