Refinement of P43212 DNA

C Squire csquire at CCU1.AUCKLAND.AC.NZ
Tue Jan 30 22:38:27 EST 1996


Hello,

I am attempting to refine a DNA octamer originally refined using
NUCLSQ.  The space group is P 43 21 2 and the asymetric unit contains 
a single strand of DNA.  The second strand is produced by 2-fold rotational
symmetry.  For NUCLSQ, a whole duplex was refined with
half occupancies and the 2 strands were averaged periodically throughout
the refinement. 

*******************************************************************
* What is the best way to deal with this refinement using X-PLOR? *
*******************************************************************

I am not very experienced in using x-plor but I have tried a couple of 
things with limited success:

1) I have tried using a single strand as the model but this results 
   in problems with the complementary strand being so close to 
   the first and being hydrogen bound.

2) I have also tried using a duplex as the model with half occupancies
   and using the NCS command with the 2 strands selected as the NCS related
   groups. This appeared useful at first but during positional refinement
   a duplex in symmetry position 5 was placed on top of a duplex
   in symmetry position 1.  These two duplexes proceeded to refine away
   from each other resulting in the R factor doubling.  I tried this
   again but with all intermolecular interactions turned off - the result
   is still not satisfactory with 2 duplexes on top of each other.


I would greatly appreciate any help!

Chris Squire.


/////////////////////////////////////////
/ Chris Squire                          /
/ Chemistry Dept.                       /
/ University of Auckland                /
/ Auckland                              /
/ New Zealand                           /
/                                       /
/ E-mail: csquire at ccu1.auckland.ac.nz   /
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