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The crystal structure of PDE8A with 1604R
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 0.1 M Cacodylate Sodium pH 6.5, 15% Isopropanol, 30% Ethylene Glycol, 8%~13% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.11 60.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.182 α = 90 b = 133.184 β = 90 c = 101.468 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 PIXEL RIGAKU HyPix-3000 2020-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2.5 22.475 99.92 0.102 19.5 8.4 18191 38.3116525847
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 99.94 0.541 3.3 7.1
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 3ECM 2.5000125483 22.4747357113 1.3652255357 18191 892 99.92309805 0.211820209914 0.210953226197 0.2188 0.228557876576 0.2349 43.3918198134
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 15.5513015261 f_angle_d 0.47851046321 f_chiral_restr 0.0354566732455 f_plane_restr 0.0039930481906 f_bond_d 0.00228200840749
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2699 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CrysalisPro data reduction