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Crystal structure of enterovirus D68-3Cpro in complex with RK-384
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 7.8, 0.2 M Ammoniumacetat, 25 % w/v PEG 3350.
Crystal Properties Matthews coefficient Solvent content 3.73 67.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.43 α = 90 b = 56.43 β = 90 c = 170.57 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 1.91 46.98 99.47 0.999 11.53 9.9 25274
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 1.91 1.978 0.323
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 1.91 46.98 25211 1262 99.467 0.232 0.2301 0.2334 0.2755 0.2643 76.362
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] 2.433 1.216 2.433 -7.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.468 r_dihedral_angle_6_deg 15.267 r_lrange_it 14.655 r_lrange_other 14.652 r_scangle_it 11.955 r_scangle_other 11.95 r_mcangle_other 9.713 r_mcangle_it 9.711 r_scbond_it 8.639 r_scbond_other 8.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.468 r_dihedral_angle_6_deg 15.267 r_lrange_it 14.655 r_lrange_other 14.652 r_scangle_it 11.955 r_scangle_other 11.95 r_mcangle_other 9.713 r_mcangle_it 9.711 r_scbond_it 8.639 r_scbond_other 8.628 r_dihedral_angle_1_deg 8.08 r_mcbond_it 7.75 r_mcbond_other 7.746 r_dihedral_angle_2_deg 7.262 r_dihedral_angle_other_3_deg 2.382 r_angle_refined_deg 1.853 r_angle_other_deg 0.653 r_symmetry_nbd_refined 0.263 r_symmetry_nbd_other 0.209 r_nbd_refined 0.206 r_nbtor_refined 0.188 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.091 r_symmetry_xyhbond_nbd_refined 0.036 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 16 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing