3BJC

Crystal structure of the PDE5A catalytic domain in complex with a novel inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RKPPDE5 catalytic domain in complex with IBMX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298The PDE5A1-12 complex was prepared by mixing 1 mM compound 12 with 15 mg/mL PDE5A1 that was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM beta-mercaptoethanol, and 1 mM EDTA. The protein drop was prepared by mixing protein with well buffer and crystallized against a well buffer of 2.0 M sodium formate, 0.1 M sodium citrate, pH 5.6, 5% ethanol at 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.755α = 90
b = 73.755β = 90
c = 132.509γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.1NSLSX29A

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
123091.10.073119.326266
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)
22.149.80.352

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 REPLACEMENTPDE5 catalytic domain in complex with IBMX2302531425340.1970.221random38.5
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_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2521
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms28

Software

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