5YX1
Crystal structure of hematopoietic prostaglandin D synthase in complex with U004
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SPRING-8 BEAMLINE BL41XU |
| Synchrotron site | SPring-8 |
| Beamline | BL41XU |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2016-11-22 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 1 |
| Unit cell lengths | 48.447, 47.119, 91.924 |
| Unit cell angles | 92.20, 98.67, 90.00 |
Refinement procedure
| Resolution | 47.940 - 1.390 |
| R-factor | 0.1863 |
| Rwork | 0.185 |
| R-free | 0.21590 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2cvd |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.566 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | MOLREP (11.0.05) |
| Refinement software | REFMAC (5.7.0029) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 70.000 | 70.000 | 1.400 |
| High resolution limit [Å] | 1.390 | 4.750 | 1.390 |
| Rmerge | 0.096 | 0.053 | 0.570 |
| Number of reflections | 144547 | 3761 | 3435 |
| <I/σ(I)> | 6.7 | ||
| Completeness [%] | 89.3 | 93.2 | 86.5 |
| Redundancy | 3.1 | 3.4 | 2.8 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | LIQUID DIFFUSION | 8.5 | 293 | 35% PEG 6000, 5 mM DTT, 2 mM MgCl2, 2 mM Glutathione, 2% Dioxane, 50 mM Tris-HCl, pH 8.5 |
