6IBF
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I04-1 |
| Synchrotron site | Diamond |
| Beamline | I04-1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2018-03-11 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.91587 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 98.476, 110.511, 160.298 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 80.110 - 2.310 |
| R-factor | 0.20621 |
| Rwork | 0.203 |
| R-free | 0.26234 |
| Structure solution method | FOURIER SYNTHESIS |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.560 |
| Data reduction software | DIALS |
| Data scaling software | Aimless |
| Phasing software | REFMAC |
| Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 80.110 | 2.370 |
| High resolution limit [Å] | 2.310 | 2.310 |
| Rmerge | 0.124 | 0.741 |
| Rmeas | 0.135 | 0.803 |
| Rpim | 0.053 | 0.307 |
| Number of reflections | 77377 | 5650 |
| <I/σ(I)> | 8.3 | 2 |
| Completeness [%] | 100.0 | 100 |
| Redundancy | 6.5 | 6.7 |
| CC(1/2) | 0.994 | 0.584 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES pH 7.5 |
