7AB9
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-656
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 | 2016-04-28 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.976250 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 99.168, 111.797, 160.261 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 91.690 - 2.190 |
R-factor | 0.187 |
Rwork | 0.185 |
R-free | 0.22290 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3sl3 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.440 |
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] | 160.260 | 2.190 |
High resolution limit [Å] | 2.180 | 2.180 |
Rmerge | 0.076 | 0.991 |
Rmeas | 0.082 | 1.075 |
Rpim | 0.032 | 0.412 |
Number of reflections | 92602 | 934 |
<I/σ(I)> | 15.9 | 1.9 |
Completeness [%] | 100.0 | 97.6 |
Redundancy | 6.6 | 6.8 |
CC(1/2) | 0.990 | 0.610 |
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 |