For this discussion another relevant reference might be:
The 1.8 A crystal structure of a statically disordered 17 base-pair
RNA duplex: principles of RNA crystal packing and its effect on
nucleic acid structure.
Shah SA, Brunger AT.
J Mol Biol. 1999 Jan 29;285(4):1577-88.
-tommi
On Jan 29, 2009, at 1:53 PM, Ian Tickle wrote:
Hi Herman
Aren't detwinning methods appropriate only in the case of true twin
domains which are larger than the X-ray photon correlation length
in order for the assumption to be valid that |F|^2 from each domain
can be summed? This wouldn't give rise to the apparent 'diffuse
scatter' phenomenon.
However if what you are describing is rather static disorder of
unit cells, which would give rise to diffuse scatter, where A & B
type cells are randomly mixed (so a domain is only one or at most a
few unit cells), as opposed to being confined to A & B type
domains, then detwinning would not be appropriate.
Cheers
-- Ian
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of
[email protected]
Sent: 29 January 2009 11:19
To: [email protected]; [email protected]
Subject: RE: [ccp4bb] Small lines in diffraction pattern (more info)
Dear Margriet,
From your description and what James Holton wrote, it seems
that you have 2 types of unit cells:
A: with the "sense" strand in position 1 and the "antisense"
strand in position 2
B: with the "antisense" strand in position 1 and the "sense"
strand in position 2
If the crystal contacts are mainly via the backbone, your
crystal may contain a random distribution of both and the
electron density you see is a superposition of both and for
the crystal packing, both chains are identical.
This situation is similar to the situation when an asymmetric
inhibitor is bound to a dimeric, symmetric molecule like e.g.
HIV protease. In this case, both orientations are
deconvoluted using detwinning methods for perfect twinning
(see e.g. Proc Natl Acad Sci U S A. 2002 November 12; 99(23):
14664-14669).
The 34,34,34 cell is definitively too small, so I would
process in the 34,34,170 cell and detwin. You molecular
replacement solutions should tell you which twinning operator to use.
Best regards,
Herman
________________________________
From: CCP4 bulletin board
[mailto:[email protected]] On Behalf Of Margriet Ovaere
Sent: Thursday, January 29, 2009 10:45 AM
To: [email protected]
Subject: Re: [ccp4bb] Small lines in diffraction
pattern (more info)
Dear all,
There were some comments about detector issues, but
these can be ruled out, to my opinion, since the lines
appeared on different beamlines.
Default settings of mosflm (spot picking) finds the
cell 34 34 34 90 90 90 (pointless indicating P41212)
Structure was solved by SAD phasing on the phosphates
in this space group. Double helices stack in continuous
helices, the backbone is well defined in the (refined)
density maps but the individual bases are messy (purines and
pyrimidines seemed to overlap) + obviously not all spots were
covered and the duplex does not fit in the A.U.
For this reason the integration was repeated in the
higher cell 34 34 170
Space group most probably P212121, but solutions can be
found in P41212 as well (still disordered bases)
There are also indications that the 41 screw axis is
rather a pseudo axis than a pure crystallographic one, also
in the small cell
Reindexing the cell to 34 34 340 also gives a solution,
which supports the theory of Holton
Rmerg is around 5% for the small cell, about 8% for the
170Å cell (both in P41212)
Which refinement procedure would be best to follow?
kind regards
Margriet
Margriet Ovaere
Chemistry Department K.U.Leuven
Biomolecular Architecture
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
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