Re: [ccp4bb] Fwd: Twinning

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Mac pro
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2009-01-06

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From: Sabuj Pattanayek sabuj {- dot -} pattanayek {- at -} VANDERBILT {- dot -} EDU
Date: 2009-01-06

Subject: Re: Fwd: Twinning
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-01-06

On Tuesday 06 January 2009 08:35:19 Stephen Hare wrote:
> Dear All,
>
> We are currently working on a structure of apparent P21 symmetry which
> has been solved by molecular replacement. The data are to 2.7Å but the
> Rfree will not drop below 30%. The density is clear for the model we
> have, however there is extra density that suggests a shift of the
> structure by 16Å in either direction - resulting in three possible
> overlapping positions for the structure. We assume this is the result
> of twinning.

It sounds like an interesting case. You might want to go back and
closely inspect your diffraction images after reading this paper:

J. Appl. Cryst. (2008). 41, 600-605
Protein crystals can be incommensurately modulated
JJ Lovelace, CR Murphy, L Daniels, K Narayan, CE Schutt,
U Lindberg, C Svensson and GEO Borgstahl

I am not certain that your description matches this case, but it might.

Ethan

> The unit cell dimensions are 102.7Å, 83.0Å, 115.3Å, 90°, 101.8°, 90°.
> Examining the data with phenix.xtriage also suggests pseudo
> translational symmetry with a separation of 16Å. A Patterson peak at
> 0.097, 0.000, -0.096 is approximately 30% of the origin peak, while a
> second peak of double the translation at 0.192, 0.000, 0.195 is 7% of
> the origin peak. The structure contains a dimer of dimers with an NCS
> 2 fold axis almost perpendicular to the crystallographic 2 fold. This
> NCS axis almost coincides with the diagonal between the A and C axes.
> A twin axis along the A C diagonal (l,-k,h) could explain the observed
> extra density, however this is not possible because A and C are
> different lengths.
>
> As a result of the NCS axis running almost perpendicular to the
> observed P21 axis, it is possible to merge the reflections in a larger
> orthorhombic unit cell - dimensions 137.1Å, 83.3Å, 169.8Å although
> here the Rmerge is higher and it is not possible to get a molecular
> replacement solution.
>
> Is it possible to define the (l,-k,h) twinning operator in our
> original unit cell? or have we missed the actual unit cell?
> Or....something else?
>
> Steve
>
>
>
> Stephen Hare PhD
> Post doctoral research associate
> Jefferiss Research Laboratories
> Wright-Fleming Institute
> Division of Medicine
> Imperial College London
> Norfolk Place
> London W2 1PG
> UK
>
> Phone: +44 (0) 20 7594 3908
> Fax: +44 (0) 20 7594 3906
>

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Mac pro
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2009-01-06

Next message:
Subject: Re: Mac pro
From: Sabuj Pattanayek sabuj {- dot -} pattanayek {- at -} VANDERBILT {- dot -} EDU
Date: 2009-01-06