4NHY
Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2013-10-07 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97949 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 108.680, 130.473, 175.784 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.238 - 2.603 |
R-factor | 0.1913 |
Rwork | 0.190 |
R-free | 0.22560 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3kt7 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.100 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | PHASER |
Refinement software | PHENIX (1.8.2_1309) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.690 |
High resolution limit [Å] | 2.600 | 5.600 | 2.600 |
Rmerge | 0.117 | 0.049 | 0.913 |
Number of reflections | 76983 | ||
<I/σ(I)> | 8.3 | 21.3 | 1.92 |
Completeness [%] | 100.0 | 99.9 | 100 |
Redundancy | 5.5 | 5.2 | 5.5 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 2.0 mM MnCl2, 2.0 mM PD2, 20% (w/v) PEG 6000, 100 mM HEPES buffer and 200 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |