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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: [log in to unmask] >> [mailto:[log in to unmask]] On Behalf Of >> [log in to unmask] >> Sent: 29 January 2009 11:19 >> To: [log in to unmask]; [log in to unmask] >> 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:[log in to unmask]] On Behalf Of Margriet Ovaere >> Sent: Thursday, January 29, 2009 10:45 AM >> To: [log in to unmask] >> 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. >> >> >> >> > > > Disclaimer > This communication is confidential and may contain privileged > information intended solely for the named addressee(s). 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