7WGN
X-ray structure of human PPAR delta ligand binding domain-pemafibrate co-crystals obtained by co-crystallization
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PHOTON FACTORY BEAMLINE BL-5A |
| Synchrotron site | Photon Factory |
| Beamline | BL-5A |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-03-20 |
| Detector | DECTRIS PILATUS3 S 6M |
| Wavelength(s) | 1.00000 |
| Spacegroup name | P 2 21 21 |
| Unit cell lengths | 37.772, 92.662, 96.760 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 37.772 - 1.813 |
| R-factor | 0.2275 |
| Rwork | 0.226 |
| R-free | 0.25480 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 3gz9 |
| RMSD bond length | 0.002 |
| RMSD bond angle | 0.589 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.5.21) |
| Phasing software | PHASER (2.7.16) |
| Refinement software | PHENIX (1.11.1-2575-000) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 48.380 | 48.380 | 1.850 |
| High resolution limit [Å] | 1.810 | 9.060 | 1.810 |
| Rmerge | 0.032 | 0.017 | 0.389 |
| Rmeas | 0.035 | 0.019 | 0.423 |
| Rpim | 0.014 | 0.007 | 0.163 |
| Total number of observations | 207167 | ||
| Number of reflections | 31614 | 314 | 1792 |
| <I/σ(I)> | 29 | 88.7 | 4.4 |
| Completeness [%] | 99.8 | 99.3 | 97.4 |
| Redundancy | 6.6 | 5.8 | 6.6 |
| CC(1/2) | 1.000 | 1.000 | 0.973 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION | 277 | 0.05 M Bis-tis propane (pH 8.5), 14% PEG8000, 0.2 M KCl, 6% propanediol, 0.001 M EDTA, 0.001 M CaCl2 |
