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Crystal structure of PDE5 in complex with inhibitor LW1805
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M Cacodylate Sodium (pH6.5), 0.2 M MgSO4, 18% PEG3350, 2.5% ethanol
Crystal Properties Matthews coefficient Solvent content 2.81 56.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.577 α = 90 b = 74.577 β = 90 c = 132.092 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 100 CCD OXFORD ONYX CCD 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 1.5406
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 2.8 24 95.74 0.132 14.1 7.9 10461
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 4MD6 2.8 24 9913 546 95.52 0.20112 0.1976 0.2045 0.26828 0.2683 RANDOM 41.812
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] -0.02 -0.01 -0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.593 r_dihedral_angle_3_deg 17.535 r_dihedral_angle_4_deg 14.837 r_long_range_B_refined 8.16 r_long_range_B_other 8.15 r_dihedral_angle_1_deg 7.988 r_mcangle_other 4.586 r_mcangle_it 4.58 r_scangle_other 4.383 r_mcbond_it 2.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.593 r_dihedral_angle_3_deg 17.535 r_dihedral_angle_4_deg 14.837 r_long_range_B_refined 8.16 r_long_range_B_other 8.15 r_dihedral_angle_1_deg 7.988 r_mcangle_other 4.586 r_mcangle_it 4.58 r_scangle_other 4.383 r_mcbond_it 2.821 r_mcbond_other 2.805 r_scbond_it 2.584 r_scbond_other 2.583 r_angle_refined_deg 1.51 r_angle_other_deg 1.001 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2499 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing