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Refinement of a model with only 50% completeness is problematic, but you have four copies of a molecule (in P1) so your molecular replacement is only looking for 24 parameters. You should be able to get a solution with 50% completeness. Dale Tronrud On 5/8/2014 1:43 PM, Yarrow Madrona wrote: > 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 <mailto: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> > [mailto: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 <mailto: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 <mailto:CCP4BB@JISCMAIL.AC.UK>] On > Behalf Of Randy Read Sent: Thursday, May 08, 2014 3:41 PM To: > CCP4BB@JISCMAIL.AC.UK <mailto: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 <tel:%2B44%201223%20336500> Wellcome Trust/MRC Building > Fax: +44 1223 336827 <tel:%2B44%201223%20336827> Hills Road > E-mail: rj...@cam.ac.uk <mailto:rj...@cam.ac.uk> Cambridge CB2 > 0XY, U.K. www-structmed.cimr.cam.ac.uk > <http://www-structmed.cimr.cam.ac.uk> > > On 8 May 2014, at 18:11, Yarrow Madrona <amadr...@uci.edu > <mailto: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 >> >> >> >> >> ____ > > __ __ > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlNr8GgACgkQU5C0gGfAG10vZwCfUTIs5Cz3fjaESFR4wh/oxlcz yygAoJmNIODJFqmM0AFQLdSCJOiYEHpJ =V2my -----END PGP SIGNATURE-----
