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Crystal structure of enterovirus D68-3Cpro in complex with RK-496
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M Tris-HCl pH 8, 0.2 M Ammonium acetate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.7 66.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.21 α = 90 b = 56.21 β = 90 c = 170.66 γ = 120
Symmetry Space Group P 31 2 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 EIGER X 16M 2026-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.08 48.68 99.87 0.999 15.07 9.8 19582
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.154 0.674
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.08 48.679 19582 980 99.883 0.202 0.2002 0.2053 0.2338 0.2405 60.368
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] 1.809 0.904 1.809 -5.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.699 r_dihedral_angle_6_deg 13.868 r_lrange_it 12.132 r_lrange_other 12.128 r_scangle_it 10.323 r_scangle_other 10.319 r_dihedral_angle_1_deg 7.631 r_dihedral_angle_2_deg 7.231 r_scbond_it 7.15 r_scbond_other 7.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.699 r_dihedral_angle_6_deg 13.868 r_lrange_it 12.132 r_lrange_other 12.128 r_scangle_it 10.323 r_scangle_other 10.319 r_dihedral_angle_1_deg 7.631 r_dihedral_angle_2_deg 7.231 r_scbond_it 7.15 r_scbond_other 7.146 r_mcangle_it 6.796 r_mcangle_other 6.786 r_dihedral_angle_other_2_deg 5.37 r_mcbond_it 5.065 r_mcbond_other 5.064 r_angle_refined_deg 1.775 r_angle_other_deg 0.677 r_dihedral_angle_other_3_deg 0.43 r_symmetry_nbd_refined 0.233 r_symmetry_nbd_other 0.207 r_nbd_refined 0.202 r_nbd_other 0.195 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.093 r_bond_refined_d 0.007 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 1469 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing