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Structure of Enterovirus A71 3C protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2 M MgCl2.6H2O
0.1 M Tris.HCl
30% PEG 4,000
Crystal Properties Matthews coefficient Solvent content 1.9 35.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.9 α = 90 b = 65.73 β = 90 c = 76.27 γ = 90
Symmetry Space Group C 2 2 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 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 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 1.341 46.166 76.6 0.075 0.999 18.2 7.8 28216
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 1.341 1.452 0.811 1.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.51 32.865 24902 1237 95.884 0.181 0.1793 0.1927 0.2101 0.2235 16.468
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] -0.595 1.051 -0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.86 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_2_deg 8.117 r_dihedral_angle_1_deg 6.984 r_lrange_it 5.915 r_lrange_other 5.845 r_scangle_it 4.366 r_scangle_other 4.364 r_scbond_it 2.855 r_scbond_other 2.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.86 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_2_deg 8.117 r_dihedral_angle_1_deg 6.984 r_lrange_it 5.915 r_lrange_other 5.845 r_scangle_it 4.366 r_scangle_other 4.364 r_scbond_it 2.855 r_scbond_other 2.853 r_mcangle_other 2.669 r_mcangle_it 2.666 r_mcbond_it 1.682 r_mcbond_other 1.681 r_angle_refined_deg 1.528 r_angle_other_deg 0.614 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.218 r_nbd_other 0.198 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.149 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.078 r_bond_other_d 0.018 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1405 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing