6BDO
Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with a quinone inhibitor HQNO at 2.8A resolution
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 |
Synchrotron site | Australian Synchrotron |
Beamline | MX2 |
Temperature [K] | 113 |
Detector technology | CCD |
Collection date | 2016-11-12 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.9537 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 72.847, 114.342, 130.061 |
Unit cell angles | 90.00, 91.17, 90.00 |
Refinement procedure
Resolution | 43.345 - 2.800 |
R-factor | 0.2293 |
Rwork | 0.227 |
R-free | 0.26810 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5wed |
RMSD bond length | 0.004 |
RMSD bond angle | 0.838 |
Data reduction software | XDS |
Data scaling software | Aimless (1.9.16) |
Phasing software | PHASER |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 43.345 | 2.890 |
High resolution limit [Å] | 2.800 | 2.800 |
Rmerge | 0.072 | 0.932 |
Rpim | 0.069 | 0.883 |
Number of reflections | 52468 | 16726 |
<I/σ(I)> | 14.5 | 1.7 |
Completeness [%] | 99.8 | 100 |
Redundancy | 3.6 | 3.7 |
CC(1/2) | 0.998 | 0.446 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | 0.1 M BICINE/TRIS BUFFER PH8.5 INCLUDING 10% (V/V) PEG 4000, 25% (V/V) ETHYLENE GLYCOL, 75 MM D,L-LYSINE, 1 MM 2-heptyl-4-hydroxyquinoline-N-oxide, 4% (V/V) dimethyl sulfoxide |