3K3E

Crystal structure of the PDE9A catalytic domain in complex with (R)-BAY73-6691


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277soaking PDE9A2-IBMX crystal in the buffer of 0.1 M HEPES pH 7.5, 3.6 M sodium formate, and 2 mM R6691 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
Crystal Properties
Matthews coefficientSolvent content
4.6873.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.19α = 90
b = 103.19β = 90
c = 270.849γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.1000NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.7301000.08412.21141185
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.81000.59100

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.7304112839257392995.50.230.230.258random57.4
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_deg1.2
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5264
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms52

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling