7A9V
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-635
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 | 99.199, 111.155, 159.684 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 91.290 - 2.170 |
R-factor | 0.191 |
Rwork | 0.189 |
R-free | 0.22920 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3sl3 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.406 |
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] | 111.150 | 2.170 |
High resolution limit [Å] | 2.160 | 2.160 |
Rmerge | 0.078 | 0.871 |
Rmeas | 0.085 | 0.941 |
Rpim | 0.033 | 0.356 |
Number of reflections | 94130 | 944 |
<I/σ(I)> | 14.9 | 2.1 |
Completeness [%] | 100.0 | 97.8 |
Redundancy | 6.7 | 6.9 |
CC(1/2) | 0.990 | 0.720 |
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 |