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Crystal structure of the PDE9 catalytic domain in complex with inhibitor 4a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1M HEPES (pH 7.5), 2.5M Na formate, 5% xylitol
Crystal Properties Matthews coefficient Solvent content 4.71 73.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.383 α = 90 b = 103.383 β = 90 c = 268.366 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 2019-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 21.872 99.67 0.177 0.187 0.058 18 8.6 57569 31.4864973288
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.8 0.716 0.779 0.304 0.82 1.8 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2HD1 2.40003752238 21.871728104 2.0139037024 57569 2834 99.6710469364 0.255448854661 0.253419807951 0.2536 0.295412615112 0.2957 35.8080136684
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.941117787 f_angle_d 1.04885446494 f_chiral_restr 0.0532399563088 f_bond_d 0.00978717664578 f_plane_restr 0.00834259955055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5266 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing