1TBF

Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T9RPDB ENTRY 1T9R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277(NH4)2SO4, PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.141.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.097α = 90
b = 76.097β = 90
c = 99.272γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102003-10-03MSINGLE 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
11.365.9499.60.06712.26.57737877378
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)
11.31.33499.20.8031.46.55747

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1T9R1.365.947737877378408599.160.15860.15860.157170.1855RANDOM10.621
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]
-0.32-0.16-0.320.48
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free8.461
r_scangle_it5.819
r_dihedral_angle_1_deg4.326
r_sphericity_bonded4.158
r_scbond_it4.018
r_mcangle_it2.594
r_rigid_bond_restr2.172
r_angle_refined_deg2
r_mcbond_it1.88
r_angle_other_deg1.485
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free8.461
r_scangle_it5.819
r_dihedral_angle_1_deg4.326
r_sphericity_bonded4.158
r_scbond_it4.018
r_mcangle_it2.594
r_rigid_bond_restr2.172
r_angle_refined_deg2
r_mcbond_it1.88
r_angle_other_deg1.485
r_symmetry_vdw_other0.425
r_symmetry_hbond_refined0.392
r_symmetry_vdw_refined0.38
r_nbd_other0.241
r_nbd_refined0.236
r_xyhbond_nbd_refined0.197
r_chiral_restr0.135
r_nbtor_other0.093
r_bond_refined_d0.025
r_gen_planes_other0.003
r_bond_other_d0.002
r_gen_planes_refined0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2637
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing