5LBO
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001
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 PILATUS3 6M |
Wavelength(s) | 0.97623 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 98.223, 111.092, 160.798 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 91.400 - 2.250 |
R-factor | 0.1754 |
Rwork | 0.174 |
R-free | 0.20965 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3sl3 |
RMSD bond length | 0.015 |
RMSD bond angle | 1.699 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0135) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 160.800 | 2.380 |
High resolution limit [Å] | 2.250 | 2.250 |
Rmerge | 0.113 | 0.763 |
Number of reflections | 80611 | |
<I/σ(I)> | 13.8 | 2.6 |
Completeness [%] | 96.4 | 100 |
Redundancy | 6.5 | 6.5 |
CC(1/2) | 0.998 |
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 |