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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
> <[log in to unmask] <mailto:[log in to unmask]>>
> 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:*[log in to unmask] <mailto:[log in to unmask]>
> [mailto:[log in to unmask] <mailto:[log in to unmask]>]
> *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
> <[log in to unmask] <mailto:[log in to unmask]>>
> wrote:____
>
> The b and c cell constants look remarkably similar....
>
> JPK____
>
>
> -----Original Message----- From: CCP4 bulletin board
> [mailto:[log in to unmask] <mailto:[log in to unmask]>] On
> Behalf Of Randy Read Sent: Thursday, May 08, 2014 3:41 PM To:
> [log in to unmask] <mailto:[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 <tel:%2B44%201223%20336500> Wellcome Trust/MRC Building
> Fax: +44 1223 336827 <tel:%2B44%201223%20336827> Hills Road
> E-mail: [log in to unmask] <mailto:[log in to unmask]> 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 <[log in to unmask]
> <mailto:[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
>>
>>
>>
>>
>> ____
>
> __ __
>
>
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