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Crystal structure of PDE4D catalytic domain complexed with compound 4e
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 7.4 277 .1 M HEPES (pH 7.4), 0.1 M MgCl2, 15-20% PEG 3350, 10% isopropanol, 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.365 α = 90 b = 77.984 β = 90 c = 163.344 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 CCD OXFORD ONYX CCD 2019-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 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 2.2 22.15 97.08 0.06 20.03 3.8 40067 24.6036207088
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 2.2 2.28 93.8 0.0337 3.137 2.9
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 FREE R-VALUE 5WQA 2.20008760676 21.9287236346 1.36630594001 39131 1897 97.969555856 0.200272535449 0.197869701281 0.1986 0.247173095303 0.249 28.5701106052
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 15.1190676021 f_angle_d 0.860596790462 f_chiral_restr 0.0445348687447 f_bond_d 0.00790651065584 f_plane_restr 0.0058795317529
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5253 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing