One thing that sometimes helps me in this situation is reprocess and refine in lower symmetry like P21. It could be you have pseudosymmetry and need to model more molecules in the AU to better reflect your data. Sometimes this can help. If that doesn't work, then you may have to stick with your 2.6 A cutoff. You are right that some reviewers might raise objections if the R-factors are too high.
Good luck, Nick On Wed, Mar 29, 2017 at 11:56 AM, Mark J van Raaij <mjvanra...@cnb.csic.es> wrote: > 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 <+34%20915%2085%2046%2016> > 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 > > > -- [This e-mail message may contain privileged, confidential and/or proprietary information of H3 Biomedicine. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.]
