☰ Navigation Tabs
Crystal structure of PDE5 in complex with inhibitor LW1634
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 0.1M Cacodylate Sodium (pH 6.5), 0.2 M MgSO4, 18% PEG3350, 2.5% ethanol
Crystal Properties Matthews coefficient Solvent content 3.07 59.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.474 α = 90 b = 74.474 β = 90 c = 132.341 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 2018-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 24.73 99.29 27.7 7.6 13486
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 2.6 2.7
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 2.6 24.73 12789 697 99.13 0.21153 0.20865 0.21 0.26436 0.2629 RANDOM 47.714
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] 0.03 0.01 0.03 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.282 r_dihedral_angle_3_deg 14.387 r_dihedral_angle_4_deg 10.771 r_long_range_B_refined 6.05 r_dihedral_angle_1_deg 5.493 r_long_range_B_other 5.393 r_mcangle_it 3.301 r_mcangle_other 3.3 r_scangle_other 3.162 r_mcbond_it 1.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.282 r_dihedral_angle_3_deg 14.387 r_dihedral_angle_4_deg 10.771 r_long_range_B_refined 6.05 r_dihedral_angle_1_deg 5.493 r_long_range_B_other 5.393 r_mcangle_it 3.301 r_mcangle_other 3.3 r_scangle_other 3.162 r_mcbond_it 1.908 r_scbond_it 1.904 r_scbond_other 1.903 r_mcbond_other 1.901 r_angle_refined_deg 1.158 r_angle_other_deg 0.896 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2418 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing