6FW3
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-007
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 | 2018-02-16 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.91587 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 99.110, 110.717, 161.490 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 65.230 - 1.780 |
R-factor | 0.17909 |
Rwork | 0.177 |
R-free | 0.21436 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3sl3 |
RMSD bond length | 0.019 |
RMSD bond angle | 1.900 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0189) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 65.230 | 1.830 |
High resolution limit [Å] | 1.780 | 1.780 |
Rmerge | 0.061 | 0.684 |
Rmeas | 0.067 | 0.759 |
Rpim | 0.026 | 0.323 |
Number of reflections | 170039 | 12471 |
<I/σ(I)> | 15 | 2 |
Completeness [%] | 100.0 | 100 |
Redundancy | 6.4 | 5.5 |
CC(1/2) | 0.999 | 0.725 |
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 |