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PanDDA analysis group deposition of ground-state model of Enterovirus D68 3Dpol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XE0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1M Tris-HCl, 16% PEG 3350, 16% Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.4 48.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.23 α = 90 b = 82.826 β = 108.62 c = 58.566 γ = 90
Symmetry Space Group P 1 21 1
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 DECTRIS EIGER2 XE 9M 2024-11-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.92202 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.34 82.98 73 0.041 1 25.3 5.18 81445
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 1.34 1.36 5.1 0.114
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5XE0 1.34 55.56 77253 4192 72.96 0.179 0.1779 0.1871 0.2001 0.2062 RANDOM 21.623
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] -0.71 0.36 0.79 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.16 r_dihedral_angle_4_deg 15.1 r_dihedral_angle_3_deg 13.093 r_dihedral_angle_1_deg 6.757 r_mcangle_it 2.829 r_mcbond_it 1.982 r_mcbond_other 1.972 r_angle_refined_deg 1.83 r_angle_other_deg 1.481 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.16 r_dihedral_angle_4_deg 15.1 r_dihedral_angle_3_deg 13.093 r_dihedral_angle_1_deg 6.757 r_mcangle_it 2.829 r_mcbond_it 1.982 r_mcbond_other 1.972 r_angle_refined_deg 1.83 r_angle_other_deg 1.481 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3639 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing