6F6J
Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/succinate/(3S)-3-hydroxy-L-lysine
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 | 2015-04-14 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97857 |
Spacegroup name | P 1 |
Unit cell lengths | 56.950, 67.390, 110.650 |
Unit cell angles | 107.55, 102.87, 93.58 |
Refinement procedure
Resolution | 40.000 - 2.000 |
R-factor | 0.196 |
Rwork | 0.194 |
R-free | 0.22500 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.010 |
RMSD bond angle | 1.020 |
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 | 0.008 | 0.833 |
Number of reflections | 101680 | 7144 |
<I/σ(I)> | 13.63 | 1.38 |
Completeness [%] | 99.0 | 93.1 |
Redundancy | 5.85 | 2.985 |
CC(1/2) | 0.998 | 0.738 |
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-KG, 0.05 M L-Lysine, 20% glycerol |