6F2B
Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/alpha-ketoglutarate
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SOLEIL BEAMLINE PROXIMA 1 |
| Synchrotron site | SOLEIL |
| Beamline | PROXIMA 1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2015-03-26 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.978570 |
| Spacegroup name | P 1 |
| Unit cell lengths | 56.820, 67.970, 110.430 |
| Unit cell angles | 107.78, 102.79, 93.45 |
Refinement procedure
| Resolution | 40.000 - 2.000 |
| R-factor | 0.173 |
| Rwork | 0.171 |
| R-free | 0.20100 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2wbq |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.000 |
| Data reduction software | XDS |
| Data scaling software | XSCALE |
| Phasing software | MOLREP |
| Refinement software | BUSTER (2.10.3) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.050 |
| High resolution limit [Å] | 2.000 | 2.000 |
| Rmeas | 0.010 | 0.113 |
| Number of reflections | 101974 | 7151 |
| <I/σ(I)> | 10.86 | |
| Completeness [%] | 98.8 | 93.7 |
| Redundancy | 3.4 | 3.4 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | KDO1: 9.3 mg/ml in 0.2 M NaCl, .001 M DTT, 0.05 M Tris-HCl, pH 8 Precipitant: 18% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate. Soaking/cryo : 20% PEG3350, 0.15 M Tris pH 7.5, 0.2 M NaCl, 0.02 M Na Succinate, 0.001 M FeIISO4 (0.5 M stock solution prepared in 0.050 M dithionite), 0.05 M alpha-ketoglutarate, 20% glycerol, 10 minute soaking |
