7Q5X
HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I24 |
Synchrotron site | Diamond |
Beamline | I24 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-07-07 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97962 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 130.454, 38.175, 42.751 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 42.750 - 1.210 |
R-factor | 0.158 |
Rwork | 0.157 |
R-free | 0.17590 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3hqr |
Data reduction software | xia2 (0.5.898) |
Data scaling software | DIALS (1.14.8) |
Phasing software | PHASER (2.8.2) |
Refinement software | PHENIX (1.19.1) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 43.480 | 43.510 | 1.230 |
High resolution limit [Å] | 1.210 | 3.280 | 1.210 |
Rmerge | 0.132 | 4.204 | |
Rmeas | 0.138 | 0.061 | 4.898 |
Rpim | 0.039 | 0.018 | 1.500 |
Number of reflections | 66301 | 3617 | 3260 |
<I/σ(I)> | 10 | 31.3 | 1 |
Completeness [%] | 100.0 | 100 | 99.1 |
Redundancy | 12.2 | 11.5 | 10.4 |
CC(1/2) | 0.999 | 0.421 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM 2OG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.33 M Magnesium formate (range: 0.25-0.39 M), 17.5% w/v polyethylene glycol 3350 (range: 18-22%); Sitting drop (200 nl): protein-to-well ratio, 1:1; Cryo-protectant: 15% v/v dilution of reservior solution with glycerol |