This case is encouraging to me that a structure can be solved with such high mosaicity (in your report is 1.9). I wonder how the diffraction looks like (I imagine spots smearing or streak). With such high mosaicity, the unit cell dimension and space group determination is highly likely not accurate. I usually lose hope of a dataset with average mosaicity above 1.3 and I would not process any high mosaic data, but from your case it seems 2.6A cutoff you get a very nice solution. It seems the data processing software (Imosflm or XDS) nowadays can handle with high mosaic data well.
On Wed, Mar 29, 2017 at 11:00 AM, Gianluca Santoni <gianluca.sant...@esrf.fr > wrote: > In addition to what Nicolas has pointed out, is it quite suspicious to me > that you have the same multiplicity in the high resolution shell as in the > low resolution. > > On Mar 29, 2017 18:17, Nicolas FOOS <nicolas.f...@esrf.fr> wrote: > > Dear Juliana, > > all the statistics presented here looks good in terms of resolution cut > (maybe I will be less sever). For me the point is about the mosaicity you > report 1.90 it's high in my opinion. How looks you images? I am wondering > if the indexation is really right. And maybe the complain of Xtriage about > outlier is due to this high mosaicity. What is the diagnostic of Xtriage in > terms of possible twinning? I am also wondering about a pseudo translation. > Maybe try to re-processed your data in this direction. > > Hope to help. > > Nicolas > > Nicolas Foos > PhD > Structural Biology Group > European Synchrotron Radiation Facility (E.S.R.F) > 71, avenue des Martyrs > CS 40220 > 38043 GRENOBLE Cedex 9+33 (0)6 76 88 14 87 <+33%206%2076%2088%2014%2087>+33 > (0)4 76 88 45 19 <+33%204%2076%2088%2045%2019> > > On 29/03/2017 17:56, Mark J van Raaij 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 > > > > >
