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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
>> 
>> 
>> 
>> 
>> ____
> 
> __ __
> 
> 
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