3K3H
Crystal structure of the PDE9A catalytic domain in complex with (S)-BAY73-6691
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS BEAMLINE X29A |
Synchrotron site | NSLS |
Beamline | X29A |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2009-06-05 |
Detector | ADSC QUANTUM 315 |
Wavelength(s) | 1.1000 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 103.272, 103.272, 271.098 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 30.000 - 2.500 |
R-factor | 0.223 |
Rwork | 0.223 |
R-free | 0.24530 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3k3e |
RMSD bond length | 0.007 |
RMSD bond angle | 1.200 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | AMoRE |
Refinement software | CNS (1.2) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 30.000 | 2.600 |
High resolution limit [Å] | 2.500 | 2.500 |
Rmerge | 0.081 | 0.570 |
Number of reflections | 51787 | |
<I/σ(I)> | 12.6 | 4.8 |
Completeness [%] | 99.9 | 100 |
Redundancy | 11.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | soaking PDE9A2-IBMX crystal in the buffer of 0.1 M HEPES pH 7.5, 3.6 M sodium formate, and 2 mM S6691 at 25 deg C for 3 days. The PDE9A2-IBMX crystals were grown by (1) mixing 10-15 mg/mL PDE9A2 catalytic domain (amino acids 181-506) with 2 mM IBMX in a buffer of 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 1 mM beta-mercaptoethanol, 1 mM EDTA, and (2) the vapor diffusion (hanging drop) at 4 deg C. The protein drops contained 2 microliters PDE9A2-IBMX complex and 2 microliters well solution of 0.1 M HEPES pH 7.5 and 3.0 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |