1XP0

Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Vardenafil


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277Sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0860.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.662α = 90
b = 89.662β = 90
c = 222.002γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102003-09-04MSINGLE 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
11.7976.796.90.0587.864665446654
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)
11.791.83696.90.5991.35.53490

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 REPLACEMENTTHROUGHOUT1.7976.74665446654252197.160.1940.193270.20788RANDOM20.466
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]
0.270.140.27-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.397
r_dihedral_angle_1_deg2.987
r_scbond_it2.253
r_angle_refined_deg1.369
r_mcangle_it1.161
r_angle_other_deg0.856
r_mcbond_it0.611
r_symmetry_vdw_other0.277
r_nbd_other0.224
r_nbd_refined0.211
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.397
r_dihedral_angle_1_deg2.987
r_scbond_it2.253
r_angle_refined_deg1.369
r_mcangle_it1.161
r_angle_other_deg0.856
r_mcbond_it0.611
r_symmetry_vdw_other0.277
r_nbd_other0.224
r_nbd_refined0.211
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.134
r_symmetry_vdw_refined0.113
r_chiral_restr0.105
r_nbtor_other0.085
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2637
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing