I am refining a lectin-carbohydrate complex. The electron density clearly
shows that a mixture of alpha- and beta-anomers of the sugar have bound in
the crystal. How can i generate appropriate restraints for the carbohydrate
with alternative conformations (i.e. alpha- and beta-anomer)? At the moment,
i use the beta-anomer dictionary from refmac for refinement. Consequently,
both conformations are pushed in the beta-position.
first off, they're not "alternative conformations" (which only differ in the
values of their torsion angles), but stereo-isomers
in principle, you could use 'floating chirality' (i.e., unrestrained improper
of the chiral carbon) but this is likely to lead to distorted geometry (i.e.,
an improper that lies somewhere in between +35 and -35 degrees).
therefore, it's probably best to use separate dictionaries for the alpha and
beta anomer and refine them as independent and different compounds (e.g., like
alpha-glucose, GLC, and beta-glucose, BGC)
--dvd
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
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