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The crystal structure of PDE4D with Amentoflavone
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% PEG3350, 10% isopropanol, 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.6 23.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.901 α = 90 b = 78.791 β = 90 c = 162.394 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 2022-06-13 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 2.1 24.52 99.78 0.133 10.6 4.4 33721 22.952731442
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 2.3 2.38 100 0.276 3.2
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 NONE 2.30003722879 24.5191488106 1.38264361064 33712 1716 99.7514498757 0.216091242956 0.213730594509 0.2206 0.258325933633 0.2677 27.1081157568
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 18.8964457887 f_angle_d 0.542346851225 f_chiral_restr 0.0363405473862 f_plane_restr 0.0033558172529 f_bond_d 0.00293427425232
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5253 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PHENIX refinement