5YWE
Crystal structure of hematopoietic prostaglandin D synthase apo form
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 | 2014-11-17 |
| Detector | DECTRIS PILATUS3 S 6M |
| Wavelength(s) | 0.9 |
| Spacegroup name | P 1 |
| Unit cell lengths | 47.429, 48.200, 88.969 |
| Unit cell angles | 95.82, 90.08, 89.97 |
Refinement procedure
| Resolution | 88.510 - 1.680 |
| R-factor | 0.171 |
| Rwork | 0.169 |
| R-free | 0.20460 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2cvd |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.195 |
| Data reduction software | MOSFLM |
| Data scaling software | Aimless (0.5.17) |
| Phasing software | MOLREP (11.0.05) |
| Refinement software | REFMAC (5.7.0029) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 88.510 | 88.510 | 1.710 |
| High resolution limit [Å] | 1.680 | 9.050 | 1.680 |
| Rmerge | 0.058 | 0.038 | 0.316 |
| Rmeas | 0.067 | 0.043 | 0.370 |
| Rpim | 0.035 | 0.022 | 0.191 |
| Total number of observations | 255531 | ||
| Number of reflections | 71217 | 558 | 3590 |
| <I/σ(I)> | 12.3 | ||
| Completeness [%] | 79.7 | 97 | 77.8 |
| Redundancy | 3.6 | 4 | 3.5 |
| CC(1/2) | 0.998 | 0.997 | 0.908 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | LIQUID DIFFUSION | 8.5 | 293 | 35% PEG 6000, 5 mM DTT, 2mM MgCl2, 2mM Glutathione, 2% Dioxane, 50 mM Tris-HCL, pH 8.5 |
