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PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z56040660
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 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.551 α = 90 b = 84.067 β = 108.1 c = 59.091 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 2024-11-16 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 1.59 84.04 98.9 0.077 0.084 0.033 0.997 11.9 5.9 68630
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 1.59 1.62 86.1 2.011 2.5 1.441 0.337 2.9
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 1.59 56.17 62687 3319 95.07 0.2137 0.2121 0.2343 0.2429 0.2609 RANDOM 35.965
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] -2.93 0.34 4 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.204 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 6.719 r_mcangle_it 3.547 r_mcbond_it 2.6 r_mcbond_other 2.594 r_angle_refined_deg 1.436 r_angle_other_deg 1.281 r_chiral_restr 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.204 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 6.719 r_mcangle_it 3.547 r_mcbond_it 2.6 r_mcbond_other 2.594 r_angle_refined_deg 1.436 r_angle_other_deg 1.281 r_chiral_restr 0.202 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 324 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing