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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z285233820
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 2.44 49.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.281 α = 90 b = 83.73 β = 108.42 c = 58.922 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 I04-1 0.92202 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 1.45 83.7 86 0.066 0.072 0.029 0.998 15.7 5.5 77522
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 1.45 1.47 35.7 1.311 1.736 1.122 0.313 2
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 1.45 55.9 73362 3922 85.81 0.1864 0.1849 0.1867 0.2155 0.2176 RANDOM 24.519
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] -0.85 0.48 1.17 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.272 r_dihedral_angle_4_deg 14.945 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 6.724 r_mcangle_it 2.773 r_mcbond_it 1.972 r_mcbond_other 1.962 r_angle_refined_deg 1.659 r_angle_other_deg 1.422 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.272 r_dihedral_angle_4_deg 14.945 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 6.724 r_mcangle_it 2.773 r_mcbond_it 1.972 r_mcbond_other 1.962 r_angle_refined_deg 1.659 r_angle_other_deg 1.422 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 322 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing