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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z1203191681
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 0.1 M TRIS-HCl (pH 8.5), 16% PEG 3350, 16% Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.599 α = 90 b = 83.807 β = 108.27 c = 59.073 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 2024-11-14 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92204 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 41.92 98 0.074 0.081 0.032 0.998 17.9 6 66485
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 76.6 1.177 1.456 0.828 0.279 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 41.94 63066 3349 98 0.1849 0.1834 0.1954 0.2118 0.2209 RANDOM 27.492
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] -1.77 0.25 2 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.458 r_dihedral_angle_4_deg 14.749 r_dihedral_angle_3_deg 13.671 r_dihedral_angle_1_deg 6.47 r_mcangle_it 2.925 r_mcbond_it 2.193 r_mcbond_other 2.185 r_angle_refined_deg 1.602 r_angle_other_deg 1.398 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.458 r_dihedral_angle_4_deg 14.749 r_dihedral_angle_3_deg 13.671 r_dihedral_angle_1_deg 6.47 r_mcangle_it 2.925 r_mcbond_it 2.193 r_mcbond_other 2.185 r_angle_refined_deg 1.602 r_angle_other_deg 1.398 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3639 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing