Re: [ccp4bb] Small lines in diffraction pattern (more info)

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

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Subject: Re: Small lines in diffraction pattern (more info)
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2009-01-29

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Subject: Re: Small lines in diffraction pattern (more info)
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-01-29

Subject: Re: Small lines in diffraction pattern (more info)
From: Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM
Date: 2009-01-29

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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Margriet Ovaere
Sent: Thursday, January 29, 2009 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK
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

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.

CCP4bb navigation

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

Previous message:
Subject: Re: Small lines in diffraction pattern (more info)
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2009-01-29

Next message:
Subject: Re: Small lines in diffraction pattern (more info)
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-01-29