The b and c cell constants look remarkably similar....

JPK

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Randy Read
Sent: Thursday, May 08, 2014 3:41 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] stalled refinement after MR solution

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: [log in to unmask]
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

On 8 May 2014, at 18:11, Yarrow Madrona <[log in to unmask]> 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
> 
> 
> 
>   
>