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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