3ZE9
3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized as-isolated state at 1.33 Angstroms
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID29 |
Synchrotron site | ESRF |
Beamline | ID29 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2011-11-21 |
Detector | DECTRIS PILATUS 6M |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 106.694, 63.348, 109.740 |
Unit cell angles | 90.00, 105.42, 90.00 |
Refinement procedure
Resolution | 52.895 - 1.330 |
R-factor | 0.132 |
Rwork | 0.131 |
R-free | 0.14780 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2wpn |
RMSD bond length | 0.012 |
RMSD bond angle | 1.303 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | PHENIX ((PHENIX.REFINE: 1.8.1_1168)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 53.900 | 1.410 |
High resolution limit [Å] | 1.330 | 1.330 |
Rmerge | 0.040 | 0.500 |
Number of reflections | 159127 | |
<I/σ(I)> | 14.2 | 1.7 |
Completeness [%] | 98.3 | 97.5 |
Redundancy | 3.1 | 3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.1 | CRYSTALS WERE OBTAINED USING THE SITTING-DROP VAPOR DIFFUSION METHOD. 1 UL OF A RESERVOIR SOLUTION CONTAINING 16% PEG 8000 (W/V) AND 0.05 M KH2PO4 PH 4.1 WAS MIXED WITH AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 11 MG/ML PROTEIN IN 20 MM TRIS-HCL BUFFER PH 7.6, AND EQUILIBRATED AGAINST A 500 UL RESERVOIR. |