Re: [ccp4bb] Fwd: Twinning

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

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Subject: Re: imosflm in ccp4 6.1.0 in linux problems
From: "Winter, G (Graeme)" graeme {- dot -} winter {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-01-07

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Subject: Re: Fwd: Twinning
From: "Isupov, Michail" M {- dot -} Isupov {- at -} EXETER {- dot -} AC {- dot -} UK
Date: 2009-01-07

Dear Steve,

Presence of several Patterson peaks at impossible (as far as crystal packing is concerned) distances
and an NCS two-fold normal to the crystallographic one suggests it could
be an order-disorder (OD) structure, like the one we had in Exeter.

An order-disorder twin crystal of L-2-haloacid dehalogenase from Sulfolobus tokodaii.
Rye CA, Isupov MN, Lebedev AA, Littlechild JA.
Acta Crystallogr D Biol Crystallogr. 2007 Aug;63(Pt 8):926-30.

For that case at 1.6 A Andrey Lebedev from York had written a dedicated detwinning (demodulation) program
and FreeR went down from 0.27 to 0.22. Original FreeR was nearly acceptable as only several percent of reflections
were overlapping.
If you feel your case appears similar to our OD-structure I would suggest you to contact Andrey, as he is collecting
cases of OD-structures and probably could modify his program for your case.

Best wishes

Misha Isupov
University of Exeter
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen Hare [s.hare@MAIL.CRYST.BBK.AC.UK]
Sent: 06 January 2009 16:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: Twinning

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

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

Previous message:
Subject: Re: imosflm in ccp4 6.1.0 in linux problems
From: "Winter, G (Graeme)" graeme {- dot -} winter {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-01-07

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Subject: nVidia Quadro FX3000 on Ubuntu 8.10
From: Chris Ulens chris {- dot -} ulens {- at -} MED {- dot -} KULEUVEN {- dot -} BE
Date: 2009-01-07