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Crystal structure of the PDE9 catalytic domain in complex with inhibitor 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 2.5M Na formate, 0.1M HEPES (pH 7.5), 5% xylitol
Crystal Properties Matthews coefficient Solvent content 4.79 74.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.11 α = 90 b = 104.11 β = 90 c = 269.079 γ = 90
Symmetry Space Group P 41 21 2
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 2018-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5418
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 2.6 25.46 99.9 0.173 10.1 6.7 46482
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 2.6 2.69 99.2 0.551 2.8 6.7
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 4QGE 2.6 25.46 44160 2292 99.79 0.24916 0.24751 0.2507 0.28022 0.2802 RANDOM 32.435
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.186 r_dihedral_angle_3_deg 15.734 r_dihedral_angle_4_deg 12.904 r_dihedral_angle_1_deg 5.818 r_long_range_B_refined 4.124 r_long_range_B_other 4.098 r_mcangle_it 2.151 r_mcangle_other 2.151 r_scangle_other 2.129 r_scbond_it 1.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.186 r_dihedral_angle_3_deg 15.734 r_dihedral_angle_4_deg 12.904 r_dihedral_angle_1_deg 5.818 r_long_range_B_refined 4.124 r_long_range_B_other 4.098 r_mcangle_it 2.151 r_mcangle_other 2.151 r_scangle_other 2.129 r_scbond_it 1.495 r_scbond_other 1.495 r_angle_refined_deg 1.249 r_mcbond_it 1.236 r_mcbond_other 1.224 r_angle_other_deg 0.929 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 5322 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing