6YVT
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2011-05-06 |
Detector | RIGAKU SATURN 944 |
Wavelength(s) | 1.5418 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 84.456, 103.018, 196.028 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 23.753 - 2.847 |
R-factor | 0.2382 |
Rwork | 0.237 |
R-free | 0.26600 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2g19 |
RMSD bond length | 0.004 |
RMSD bond angle | 0.795 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHASER |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.950 |
High resolution limit [Å] | 2.847 | 6.140 | 2.850 |
Rmerge | 0.180 | 0.088 | |
Rmeas | 0.200 | 0.097 | |
Rpim | 0.112 | 0.039 | 0.710 |
Number of reflections | 40604 | 4243 | 4007 |
<I/σ(I)> | 6.71 | 1.81 | |
Completeness [%] | 99.4 | 97.7 | 99.6 |
Redundancy | 5.3 | 6.1 | 5 |
CC(1/2) | 0.998 | 0.998 | 0.482 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol. |