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Crystal structure of PDE8A catalytic domain in complex with 2c
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 3.35 62.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.114 α = 90 b = 131.874 β = 90 c = 101.398 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 2020-07-30 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 23.66 99.5 0.068 22.16 5 12282
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 2.8 2.9 100 0.256 5.52 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ECM 2.8 23.66 12244 622 99.56 0.25851 0.25675 0.29258 0.2212 RANDOM 47.217
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] -3.91 -1.77 5.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 11.184 r_dihedral_angle_4_deg 10.77 r_dihedral_angle_1_deg 4.392 r_long_range_B_refined 2.855 r_long_range_B_other 2.836 r_mcangle_it 1.272 r_mcangle_other 1.271 r_angle_refined_deg 0.921 r_angle_other_deg 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 11.184 r_dihedral_angle_4_deg 10.77 r_dihedral_angle_1_deg 4.392 r_long_range_B_refined 2.855 r_long_range_B_other 2.836 r_mcangle_it 1.272 r_mcangle_other 1.271 r_angle_refined_deg 0.921 r_angle_other_deg 0.844 r_mcbond_it 0.677 r_mcbond_other 0.677 r_scangle_other 0.668 r_scbond_it 0.32 r_scbond_other 0.32 r_chiral_restr 0.048 r_bond_refined_d 0.007 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 2727 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing