6THE
Crystal structure of core domain of four-domain heme-cupredoxin-Cu nitrite reductase from Bradyrhizobium sp. ORS 375
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I24 |
Synchrotron site | Diamond |
Beamline | I24 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-02-17 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9686 |
Spacegroup name | I 2 3 |
Unit cell lengths | 125.141, 125.141, 125.141 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 39.570 - 2.870 |
R-factor | 0.2257 |
Rwork | 0.225 |
R-free | 0.23440 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2dv6 |
RMSD bond length | 0.002 |
RMSD bond angle | 0.653 |
Data scaling software | xia2 (0.5.769) |
Phasing software | MOLREP (11.6.04) |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 39.570 | 3.030 |
High resolution limit [Å] | 2.870 | 2.870 |
Rmerge | 0.219 | 0.481 |
Rmeas | 0.275 | 0.607 |
Rpim | 0.163 | 0.362 |
Number of reflections | 7073 | 958 |
<I/σ(I)> | 3.5 | 1.7 |
Completeness [%] | 93.2 | 88.8 |
Redundancy | 2.8 | 2.6 |
CC(1/2) | 0.939 | 0.738 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 10% (w/v) PEG 8,000, 20% (v/v) 1,5-pentanediol, 0.1 M MOPSO/Bis-Tris pH6.5, 0.005 M Yttrium (III) chloride hexahydrate, 0.005 M Erbium (III) chloride hexahydrate, 0.005 M Terbium (III) chloride hexahydrate, 0.005 M Ytterbium (III) chloride hexahydrate |