6YW4
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I02 |
Synchrotron site | Diamond |
Beamline | I02 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-09-17 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9795 |
Spacegroup name | P 65 |
Unit cell lengths | 46.622, 46.622, 203.711 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 39.605 - 1.528 |
R-factor | 0.1628 |
Rwork | 0.162 |
R-free | 0.17700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5l9r |
RMSD bond length | 0.016 |
RMSD bond angle | 1.407 |
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 | 1.580 |
High resolution limit [Å] | 1.528 | 3.500 | 1.530 |
Rmerge | 0.124 | 0.071 | |
Rmeas | 0.129 | 0.074 | |
Rpim | 0.039 | 0.020 | 0.532 |
Number of reflections | 37807 | 3209 | 3124 |
<I/σ(I)> | 20.07 | 1.73 | |
Completeness [%] | 100.0 | 99.9 | 100 |
Redundancy | 16 | 13.1 | 13.1 |
CC(1/2) | 0.996 | 0.996 | 0.653 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 8.5, 1.26 M ammonium sulfate; Sitting drop (300 nl), protein-to-well ratio, 1:1 |