Hi Yarrow, If Dale said that, he probably wasn’t saying what he meant clearly enough! The NCS 2-fold axis has to be parallel to the crystallographic 2-fold (screw) axis to generate tNCS. In your case, the NCS is a 2-fold approximately parallel to the y-axis, but it’s nearly 9 degrees away from being parallel to y. That explains why the Patterson peak is so small, and there will be very little disruption from the statistical effects of tNCS.
The anisotropy could be an issue. It might be interesting to look at the R-factors for the stronger subset of the data. It can make sense to apply an elliptical cutoff of the data using the anisotropy server (though Garib says that having systematically incomplete data can create problems for Refmac), but I hope you’re not using the anisotropically scaled data for refinement. The determination of the anisotropic B-factors by Phaser without a model (underlying the anisotropy server) will not be as accurate as what Refmac or phenix.refine can do with a model. Finally, as Phil Evans always says, the space group is just a hypothesis, so you should always be willing to go back and look at the evidence for the space group if something doesn’t work as expected. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 8 May 2014, at 18:11, Yarrow Madrona <amadr...@uci.edu> wrote: > Hello CCP4 community, > > I am stumped and would love some help. I have a molecular replacement > solution that has Rfree stuck around 40% while Rwork is aorund 30%. The model > is actually the same enzyme with a similar inhibitor bound. Relevant > information is below. > > -Yarrow > > I have solved a structure in a P21 spacegroup: > > 51.53 88.91 89.65, beta = 97.1. > > Processing stats (XDS) are very good with low Rmerge (~5% overall) and good > completeness. > > I don't think twinning is an option with these unit cell dimensions. My data > was highly aniosotropic. I ran the data through the UCLA anisotropic server > to scale in the B- direction (http://services.mbi.ucla.edu/anisoscale/) > > I get a small (a little over 5) patterson peak suggesting there is not much > t-NCS to worry about. However, the output structure does have 2 fold symmetry > (see below) and as Dale Tronrud pointed out, there is always tNCS in a P21 > space group with two monomers related by a 2-fold axis. > I calculated the translation to be unit cell fractions of 0.36 0.35, 0.32. > > rota_matrix -0.9860 -0.1636 -0.0309 > rota_matrix -0.1659 0.9511 0.2605 > rota_matrix -0.0132 0.2620 -0.9650 > tran_orth 34.3310 -24.0033 107.0457 > > center_orth 15.7607 7.2426 77.7512 > > Phaser stats: > SOLU SET RFZ=20.3 TFZ=19.5 PAK=0 LLG=1314 RF++ TFZ=63.8 PAK=0 LLG=4745 > LLG=4947 > > > > >
