Re: [ccp4bb] Fwd: Twinning

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

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Subject: Re: Fwd: Twinning
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2009-01-07

Hey Stephen,

how about simply putting three models, separated by 16A, into your
original unit cell and refining them together. You'd have to guess
their fractional occupancies from the heights of the Patterson peaks
(and make them add up to one, obviously).

This approach (in contrast to correcting the intensities) was the
consensus when I talked to Peter Zwart and Tom Terwilliger about a
similar problem. As my problem still hasn't been solved (probably
because of flawed data processing due to overlapping spots), I'd be very
keen on hearing about your progress.

http://scripts.iucr.org/cgi-bin/paper?S0907444908016648
describes both approaches to lattice-translocated crystals (correcting
intensities and refining several models concurrently).

http://scripts.iucr.org/cgi-bin/paper?ba5111
is the best review on the subject.

All the best.

Andreas

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.
>
> 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
>

--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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

Previous message:
Subject: Re: nVidia Quadro FX3000 on Ubuntu 8.10
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
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Next message:
Subject: Re: imosflm in ccp4 6.1.0 in linux problems
From: Harry Powell harry {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-01-07