6ZBA
Crystal structure of PDE4D2 in complex with inhibitor LEO39652
This is a non-PDB format compatible entry.
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 | 2019-09-23 |
Detector | DECTRIS EIGER2 X 9M |
Wavelength(s) | 0.9159 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 100.030, 111.866, 159.623 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 79.939 - 1.600 |
Rwork | 0.162 |
R-free | 0.19180 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1y2k |
RMSD bond length | 0.010 |
RMSD bond angle | 1.590 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 79.939 | 1.630 |
High resolution limit [Å] | 1.600 | 1.600 |
Rmerge | 0.085 | 1.481 |
Number of reflections | 235229 | 11558 |
<I/σ(I)> | 9.2 | 1 |
Completeness [%] | 100.0 | 100 |
Redundancy | 6.6 | 6 |
CC(1/2) | 0.997 | 0.422 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | Protein stored at 20.6 mg/mL in a storage buffer of 50 mM NaCl, 20 mM Tris HCl (pH 7.5), 1 mM TCEP, 1 mM EDTA. Reservoir was 0.1 M HEPES (pH 7.5), 19% PEG3350, 25% ethylene glycol, 5% 2-propanol, 5% glycerol. Drops were microseeded. Apo crystals were soaked with 0.8 mM LEO39652A for 3 days. |