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Crystal structure of PDE8A catalytic domain in complex with 10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ECM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 100mM Cacodylate Sodium pH 6.5, 15% Isopropanol, 30% Ethylene Glycol, 11% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.25 62.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.089 α = 90 b = 131.662 β = 90 c = 101.507 γ = 90
Symmetry Space Group C 2 2 21
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 2020-11-19 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 2.5 24.19 99.2 0.07 20.18 4.8 17903 38.0511836313
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 2.5 2.59 0.272
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 THROUGHOUT 3ECM 2.50006900162 24.1876565841 1.96594775955 17869 903 99.2446542627 0.226792455724 0.224984393664 0.226 0.259221248638 0.2602 46.4085779979
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 12.3739467226 f_angle_d 0.975740438965 f_chiral_restr 0.0487377215909 f_bond_d 0.00947233376581 f_plane_restr 0.00622639778983
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2735 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing REFMAC refinement