Hi Jacob. I am worried that I would dramatically suffer in data completeness. I am not sure how reliable the data is when you are have 50% completeness. These crystals are also pretty much impossible to reproduce at the moment.
On Thu, May 8, 2014 at 1:30 PM, Keller, Jacob <kell...@janelia.hhmi.org>wrote: > Since your search model is so good, why not go down to p1 to see what’s > going on, then re-merge if necessary? > > > > JPK > > > > *From:* yarrowmadr...@gmail.com [mailto:yarrowmadr...@gmail.com] *On > Behalf Of *Yarrow Madrona > *Sent:* Thursday, May 08, 2014 4:29 PM > *To:* Keller, Jacob > > *Subject:* Re: [ccp4bb] stalled refinement after MR solution > > > > I have had problems in the past with a and c cell being equal and having > pseudo-merhohedral twining where the space group looked like C2221 but the > true space group was P21 (near perfect 2fold NCS). But I didn't think > twining was possible in this case. > > > > On Thu, May 8, 2014 at 12:43 PM, Keller, Jacob <kell...@janelia.hhmi.org> > wrote: > > The b and c cell constants look remarkably similar.... > > JPK > > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Randy Read > Sent: Thursday, May 08, 2014 3:41 PM > To: CCP4BB@JISCMAIL.AC.UK > 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: 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 > > > > > > > > > > > > >
