On Sunday 28 January 2007 08:38, Gerard DVD Kleywegt wrote:
> > 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).
That would be true were it not for the cleverness of whoever set up
the sugar restraint system for refmac. The syntax allows you to set the
chirality restraint on the anomeric sugar to "both". This restrains to the
correct absolute value of the chiral volume, thus accepting either anomer.
I have succesfully refined structures with mixed sugar anomers
present using this mechanism. Admittedly this was several refmac versions
back, but so far as I know the current version should be at least as
accepting as the older versions were.
Here is a fragment of one such cif dictionary file:
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
NGA chir_01 C1 C2 O1 O5 both
NGA chir_02 C2 C1 C3 N2 negativ
NGA chir_03 C3 C2 C4 O3 positiv
NGA chir_04 C4 C3 C5 O4 positiv
NGA chir_05 C5 C4 C6 O5 negativ
Ethan
>
> 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
>
> ******************************************************************
> 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]
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
