☰ Navigation Tabs
Crystal structure of PDE8A catalytic domain in complex with 15
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% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.25 62.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.986 α = 90 b = 131.724 β = 90 c = 101.456 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 2020-04-06 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 24.17 99.5 0.083 18.11 4.1 12854 32.9169773754
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 0.208
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 2.8 24.17 1.97088197898 12846 677 99.8135198135 0.284233983237 0.282016164852 0.2847 0.324406094087 0.3204 30.0212259444
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 17.3649792554 f_angle_d 1.09578227925 f_chiral_restr 0.0540706623665 f_bond_d 0.00784731405636 f_plane_restr 0.00370165366427
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2721 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing