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Crystal structure of PDE4D catalytic domain complexed with compound 23a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1 M Hepes (pH 7.4), 0.1 M MgCl2, 15% PEG 3350, 10% isopropanol, 25% ethylene glycol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.057 α = 90 b = 80.416 β = 90 c = 162.918 γ = 90
Symmetry Space Group P 21 21 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 2022-01-06 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 2.1 24.34 99.8 0.084 14.1 4.8 45273
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 2.1 2.18 100 0.293 3.4 3.3
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 5WQA 2.10000900931 24.3365211701 1.36559810472 45271 2226 99.7905920734 0.212801294238 0.211212919331 0.2113 0.243531009297 0.2445 24.3573805474
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 15.3732934847 f_angle_d 1.02675817038 f_chiral_restr 0.0415689404997 f_bond_d 0.00665054376986 f_plane_restr 0.00561835929021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5230 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing