To be really convinced I think you should also compare the maps at 2.6 and 2.3 Å. If the 2.3 Å map looks better, go for it. If it doesn’t look better, perhaps you are adding noise, but the I/sigma and CC1/2 values suggest you aren’t. Perhaps try 2.5 and 2.4 Å also. And perhaps remove a well-ordered aa from the input model, refine at different resolutions and compare the difference maps for that aa. Or calculate omit maps at different resolutions and compare those.
Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://wwwuser.cnb.csic.es/~mjvanraaij > On 29 Mar 2017, at 17:44, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: > > 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
