NAD & b-factors > 100A2

Jordi Benach jordi.benach at csb.ki.se
Mon Jul 21 06:54:19 EST 1997


Dear x-plor users,

I'm refining a structure of a complex at 2.6 A resolution. The enzyme
is complexed with NAD and an inhibitor. And one can see clearly the
molecule of NAD+ in Fo-Fc maps without any problem.

In order to avoid problems with "O". I renamed the atoms in the NAD+
molecule to my own ones (like C1, C2, .. N1, N2... O1, O2... etc)
and change the corresponding xplor topology.nad file.

Then I divide the molecule in several pieces to fit easier the molecule
into the density.

Do model building and assemble the pieces to a single regular NAD+
molecule, finally do some positional refinement cycles.. it usually
refines the molecule away from the electron density.(??? I wonder)

When I do group b-factor refinement of the NAD+ molecule, the value
gets about 100 A2? If I try individual b-factor refinement -only for
the NAD+ molecule- some atoms get as well 100 A2 as b-factor.

Could someone give me a hint?

Thanks,

JB



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