 |
PDBsum entry 3kyv
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Electron transport
|
PDB id
|
|
|
|
3kyv
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Unambiguous determination of h-Atom positions: comparing results from neutron and high-Resolution X-Ray crystallography.
|
|
|
Authors
|
|
A.S.Gardberg,
A.R.Del castillo,
K.L.Weiss,
F.Meilleur,
M.P.Blakeley,
D.A.Myles.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 2010,
66,
558-567.
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The locations of H atoms in biological structures can be difficult to determine
using X-ray diffraction methods. Neutron diffraction offers a relatively greater
scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron
diffraction studies of fully perdeuterated and selectively CH(3)-protonated
perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and
HD-rubredoxin, respectively) at room temperature (RT) are described, as well as
1.1 A resolution X-ray diffraction studies of the same protein at both RT and
100 K. The two techniques are quantitatively compared in terms of their power to
directly provide atomic positions for D atoms and analyze the role played by
atomic thermal motion by computing the sigma level at the D-atom coordinate in
simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT
neutron data for perdeuterated rubredoxin are approximately 8 times more likely
overall to provide high-confidence positions for D atoms than 1.1 A resolution
X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint
X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the
D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The
X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and
8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and
HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint
XN refinement yielded improved electron-density maps, permitting the location of
more D atoms than electron-density maps from models refined against X-ray data
only.
|
|
|
|
|
|
|
