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The crystal structure of PDE4D with Pinoresinol Dimethyl Ether
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 0.1M HEPES (pH 7.4), 0.1M MgCl2, 15-18% PEG3350, 10% isopropanol, 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.692 α = 90 b = 80.089 β = 90 c = 163.001 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 2022-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54056
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 23.16 98.7 0.064 14.3 4.1 44338 21.57
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 2.2 100 0.186
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 23.16 1.39 44333 2204 98.73 0.2083 0.2059 0.2102 0.2555 0.2597 25.81
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 15.7713 f_angle_d 0.4978 f_chiral_restr 0.0346 f_plane_restr 0.004 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5226 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CrysalisPro data reduction Aimless data scaling PHASER phasing