6TP5
Crystal structure of human Transmembrane prolyl 4-hydroxylase
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-12-19 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.976 |
Spacegroup name | P 31 |
Unit cell lengths | 92.079, 92.079, 129.500 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 50.300 - 2.250 |
R-factor | 0.1829 |
Rwork | 0.181 |
R-free | 0.22130 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2jig |
RMSD bond length | 0.005 |
RMSD bond angle | 0.696 |
Data reduction software | XDS (Mar 15, 2019) |
Data scaling software | XDS (Mar 15, 2019) |
Phasing software | PHASER (2.8.3) |
Refinement software | PHENIX (1.15.2_3472) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.300 | 2.330 |
High resolution limit [Å] | 2.250 | 2.250 |
Rmerge | 0.092 | 1.950 |
Rmeas | 0.109 | 2.380 |
Rpim | 0.057 | 1.340 |
Number of reflections | 57041 | 4799 |
<I/σ(I)> | 7.35 | 0.4 |
Completeness [%] | 98.0 | 83 |
Redundancy | 3.4 | 2.7 |
CC(1/2) | 0.995 | 0.180 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 277 | Well solution: 0.1 M Tris-HCl pH 9, 22% Tert-butanol, 1 mM N-oxalylglycine Protein solution: 10 mM Tris-HCl pH 7.8, 0.1 M NaCl, 0.1 M Glycine, 2 mM CaCl2, 0.02 mM FeSO4 |