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[ccp4bb]: REFMAC dictionaries etc
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Dear All,
We are refining a structure at 1.54A resolution.
We know we have NADH bound and the original Fo-Fc density shows the ring is
distorted into a boat.
Refining B's isotropically ends up with the ring in a twist boat
conformation (even although it is planar restrained). Obviously this is well
and good. So I reconstructed the dictionary by removing planar restraint and
adjusting some bond lengths and angles. Dihedral angles I widened the
restraints for. The result is the NADH now becomes a chair (bad).
Also anisotropic refinement causes the ring to flatten out with my new slack
restraints.
(The form of NADH we have is opposite in the pro chirality of the hydride to
the Lamzin et al JBC)
Any thoughts welcomed!
To summarise external spec data shows NADH, initial density shows NADH is in
a boat form but at 1.5A it is not possible accurately position each atom.
Isotropic B-factor refinement (R-fac 17 & 14%) give a boat. How do we
formulate restraints etc?
Secondly we are trying install Ethan Merrits program to look at thermal
ellipsoids (which may be distorted) but at first glance with the weakened
dictionary this causes the ring to flatten out. The distortion in the ring
will be small, could it be soaked up by error in the ellipsoids?.
best
Jim
James H. Naismith | Research mailto:naismith@st-and.ac.uk
Professor of Chemical Biology | Teaching mailto:jhn@st-and.ac.uk
BBSRC Career Development Fellow |
Centre for Biomolecular Sciences | Office: 1334-463792 (24 hr)
The North Haugh | Fax : 1334-467229
The University | Lab : 1334-467245
St. Andrews | In UK add 0 to start of number
Fife Scotland, U.K., KY16 9ST | www http://speedy.st-and.ac.uk/