7ABJ
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1361
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2016-09-12 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97622 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 98.999, 111.037, 160.565 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 84.410 - 2.110 |
R-factor | 0.1828 |
Rwork | 0.181 |
R-free | 0.21780 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3sl3 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.483 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 160.565 | 2.143 |
High resolution limit [Å] | 2.107 | 2.107 |
Rmerge | 0.061 | 0.800 |
Rmeas | 0.066 | 0.870 |
Rpim | 0.026 | 0.339 |
Number of reflections | 102569 | 5080 |
<I/σ(I)> | 17.5 | 2.2 |
Completeness [%] | 99.9 | 99.5 |
Redundancy | 6.6 | 6.5 |
CC(1/2) | 0.999 | 0.741 |
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 |