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Structure of Enterovirus D68 3C protease
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 8.14 293 25% PEG 3,350
0.1 M Tris
0.2 M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.31 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.82 α = 90 b = 62.53 β = 90 c = 147.36 γ = 90
Symmetry Space Group P 21 21 21
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 X 9M 2023-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.49 38.63 91.9 0.099 0.998 11.4 10.5 60463
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 1.49 1.53 56.7 0.388 0.7 4.1
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 1.49 38.627 60384 3016 92.043 0.204 0.2036 0.2125 0.2199 0.2252 25.167
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] -1.2 2.642 -1.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.856 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_1_deg 7.312 r_lrange_it 6.526 r_lrange_other 6.511 r_dihedral_angle_2_deg 6.348 r_scangle_it 5.24 r_scangle_other 5.238 r_mcangle_other 3.525 r_mcangle_it 3.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.856 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_1_deg 7.312 r_lrange_it 6.526 r_lrange_other 6.511 r_dihedral_angle_2_deg 6.348 r_scangle_it 5.24 r_scangle_other 5.238 r_mcangle_other 3.525 r_mcangle_it 3.523 r_scbond_it 3.518 r_scbond_other 3.517 r_mcbond_it 2.666 r_mcbond_other 2.642 r_angle_refined_deg 1.581 r_angle_other_deg 0.902 r_symmetry_xyhbond_nbd_refined 0.321 r_symmetry_nbd_refined 0.282 r_nbd_refined 0.225 r_symmetry_nbd_other 0.201 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.173 r_xyhbond_nbd_other 0.143 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_other_d 0.036 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2808 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing