6TFD
Crystal structure of nitrite and NO bound three-domain copper-containing nitrite reductase from Hyphomicrobium denitrificans strain 1NES1
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04 |
Synchrotron site | Diamond |
Beamline | I04 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-06-29 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.9795 |
Spacegroup name | P 65 2 2 |
Unit cell lengths | 77.722, 77.722, 758.201 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 126.370 - 2.250 |
R-factor | 0.1747 |
Rwork | 0.172 |
R-free | 0.22710 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2dv6 |
RMSD bond length | 0.007 |
RMSD bond angle | 1.601 |
Data reduction software | autoPROC |
Data scaling software | Aimless (0.7.4) |
Phasing software | MOLREP (11.6.04) |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 126.370 | 2.140 |
High resolution limit [Å] | 2.100 | 2.100 |
Rmerge | 0.216 | 2.845 |
Rpim | 0.064 | 0.828 |
Number of reflections | 81889 | 3922 |
<I/σ(I)> | 7.7 | 0.855 |
Completeness [%] | 100.0 | 100 |
Redundancy | 12.1 | 12.3 |
CC(1/2) | 0.998 | 0.426 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.3 | 298 | 22.5% (v/v) PEG Smear Low, 0.1 M Sodium cacodylate pH5.3 0.2 M Ammonium nitrate |