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Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T9R PDB ENTRY 1T9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 (NH4)2SO4, PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.097 α = 90 b = 76.097 β = 90 c = 99.272 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 210 2003-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.3 65.94 99.6 0.067 12.2 6.5 77378 77378
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.334 99.2 0.803 1.4 6.5 5747
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1T9R 1.3 65.94 77378 77378 4085 99.16 0.1586 0.1586 0.15717 0.2386 0.1855 0.2577 RANDOM 10.621
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 -0.32 0.48
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 8.461 r_scangle_it 5.819 r_dihedral_angle_1_deg 4.326 r_sphericity_bonded 4.158 r_scbond_it 4.018 r_mcangle_it 2.594 r_rigid_bond_restr 2.172 r_angle_refined_deg 2 r_mcbond_it 1.88 r_angle_other_deg 1.485
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 8.461 r_scangle_it 5.819 r_dihedral_angle_1_deg 4.326 r_sphericity_bonded 4.158 r_scbond_it 4.018 r_mcangle_it 2.594 r_rigid_bond_restr 2.172 r_angle_refined_deg 2 r_mcbond_it 1.88 r_angle_other_deg 1.485 r_symmetry_vdw_other 0.425 r_symmetry_hbond_refined 0.392 r_symmetry_vdw_refined 0.38 r_nbd_other 0.241 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.135 r_nbtor_other 0.093 r_bond_refined_d 0.025 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_gen_planes_refined 0.002 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 Atoms Number Protein Atoms 2637 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection ELVES data scaling EPMR phasing