1XOZ

Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Tadalafil


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0138.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.102α = 90
b = 76.397β = 103.18
c = 80.699γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102003-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1ALS8.3.1

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
11.3779.0697.380.0776.73.46426364263
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)
1.371.40696.20.8941.42.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTTHROUGHOUT1.3779.066426364263341697.380.15410.152030.19335RANDOM10.348
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]
-0.24-0.180.37-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free6.552
r_scangle_it6.453
r_dihedral_angle_1_deg4.517
r_scbond_it4.331
r_sphericity_bonded3.398
r_mcangle_it2.79
r_rigid_bond_restr2.411
r_angle_refined_deg1.92
r_mcbond_it1.807
r_angle_other_deg1.114
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free6.552
r_scangle_it6.453
r_dihedral_angle_1_deg4.517
r_scbond_it4.331
r_sphericity_bonded3.398
r_mcangle_it2.79
r_rigid_bond_restr2.411
r_angle_refined_deg1.92
r_mcbond_it1.807
r_angle_other_deg1.114
r_symmetry_vdw_refined0.37
r_symmetry_hbond_refined0.342
r_symmetry_vdw_other0.302
r_nbd_other0.245
r_nbd_refined0.235
r_chiral_restr0.199
r_xyhbond_nbd_refined0.193
r_nbtor_other0.093
r_bond_refined_d0.024
r_bond_other_d0.002
r_gen_planes_refined0.001
r_gen_planes_other0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2637
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing