1PD2
CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-6A |
Synchrotron site | Photon Factory |
Beamline | BL-6A |
Temperature [K] | 298 |
Detector technology | IMAGE PLATE |
Detector | RIGAKU |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 56.500, 56.500, 233.400 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 6.000 - 2.300 |
R-factor | 0.204 * |
Rwork | 0.204 |
R-free | 0.28900 |
Structure solution method | MIRAS |
RMSD bond length | 0.010 |
RMSD bond angle | 1.613 |
Data reduction software | ROTAVATA |
Data scaling software | WEIS |
Phasing software | PHASES |
Refinement software | X-PLOR (3.1) |
Data quality characteristics
Overall | |
Low resolution limit [Å] | 40.000 |
High resolution limit [Å] | 2.300 |
Rmerge | 0.085 |
Number of reflections | 77899 |
Completeness [%] | 95.1 |
Redundancy | 4 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | Vapor diffusion, hanging drop * | 7.5 * | 22.5 * | VAPOR DIFFUSION METHOD RESERVOIR SOLUTION: 18% (W/V) PEG 6K, 100 MM AMMONIUM CITRATE 5MM CACL2, 10MM DTT, 2% (V/V) 1,4-DIOXANE PROTEIN SOLUTION: 7.3 MG/ML PROTEIN (50 MM TRIS-HCL [PH 7.5]) EACH 4 UL WAS MIXED FOR DROPLET |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | 7.3 MG/ML PROTEIN (50 MM TRIS-HCL [PH 7.5}) | ||
2 | 1 | 2 | 10% (W/V) PEG 6K | ||
3 | 1 | 2 | 100 MM AMMONIUM CITRATE | ||
4 | 1 | 2 | 5MM CACL2 | ||
5 | 1 | 2 | 10MM DTT | ||
6 | 1 | 2 | 2% (V/V) 1,4-DIOXANE |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | protein | 7.3 (mg/ml) | |
2 | 1 | drop | Tris-HCl | 50 (mM) | |
3 | 1 | drop | GSH | 10 (mM) | |
4 | 1 | reservoir | PEG6000 | 18 (%(w/v)) | |
5 | 1 | reservoir | ammonium citrate | 100 (mM) | |
6 | 1 | reservoir | 5 (mM) | ||
7 | 1 | reservoir | dithiothreitol | 10 (mM) | |
8 | 1 | reservoir | 1,4-dioxane | 2 (%(v/v)) |