5OHJ
Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor.
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 | 2012-10-31 |
Detector | DECTRIS PILATUS 2M |
Wavelength(s) | 0.92 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 55.270, 55.730, 225.560 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.610 - 1.600 |
R-factor | 0.18549 |
Rwork | 0.184 |
R-free | 0.21153 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | dimer of the catalytic domain of PDE4D |
RMSD bond length | 0.019 |
RMSD bond angle | 1.880 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | REFMAC (5.7.0029) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 29.610 | 1.550 |
High resolution limit [Å] | 1.510 | 1.510 |
Rmerge | 0.046 | 0.467 |
Rpim | 0.041 | 0.149 |
Number of reflections | 85681 | 2246 |
<I/σ(I)> | 22.4 | 2.6 |
Completeness [%] | 77.7 | 28.3 |
Redundancy | 6.4 | 3.7 |
CC(1/2) | 0.999 | 0.791 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | Drops comprised 2microliters protein solution mixed with reservoir buffer consisting of 100mM sodium acetate pH 4.5, 14% PEG400 and 50mM calcium acetate. After 2 days they were streak seeded with crystals obtained from rolipram complex seed stock. Crystals, up to 100 microns in largest dimension, grew from precipitate after 1-2 weeks. Crystals were transferred to a cryoprotectant solution (100mM sodium acetate pH 4.5, 14% PEG400, 50mM calcium acetate and 20% glycerol) then flash-frozen prior to X-ray data collection. |