4QGE

phosphodiesterase-9A in complex with inhibitor WYQ-C36D


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277The crystals of PDE9A2 were grown by using hanging drop vapor diffusion method. The PDE9A2 (181 506) (8-10 mg/mL) in a buffer of 50 mM NaCl, 20 mM Tris HCl, pH 7.5, 1 mM -mercaptoethanol, and 1 mM EDTA was mixed with 2 mM IBMX overnight before setting-up of crystallization against the well buffer of 0.1 M HEPES (pH 7.5), 3.0 M sodium formate at 4 C. Crystals of the PDE9-3r complex were prepared by soaking PDE9-IBMX cocrystals in the crystallization buffer plus 2 mM 3r at 25oC for 3 days., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9257.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.58α = 90
b = 103.58β = 90
c = 268.657γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.05NSLSX29A

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
123091.50.0652310.591112

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDE9 catalytic domain2309106890980.2410.268random
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_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5304
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms62

Software

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