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Crystal structure of Enterovirus 71 2A protease mutant C110A containing VP1-2A junction in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8POA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.1M Sodium chloride, 15% ethanol
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.544 α = 90 b = 61.544 β = 90 c = 78.932 γ = 120
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 9M 2024-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.43 28.69 99.8 0.056 0.057 0.013 1 30.2 18.8 31516
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 1.43 1.45 96.9 0.726 0.773 0.262 0.843 8.5
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 MOLECULAR REPLACEMENT THROUGHOUT 1.43 28.69 30029 1443 99.83 0.15203 0.1514 0.1613 0.16478 0.177 RANDOM 18.566
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] 0.24 0.12 0.24 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_4_deg 17.089 r_dihedral_angle_3_deg 11.414 r_dihedral_angle_1_deg 7.601 r_long_range_B_refined 4.756 r_long_range_B_other 4.588 r_scangle_other 2.672 r_scbond_it 1.928 r_scbond_other 1.922 r_angle_refined_deg 1.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_4_deg 17.089 r_dihedral_angle_3_deg 11.414 r_dihedral_angle_1_deg 7.601 r_long_range_B_refined 4.756 r_long_range_B_other 4.588 r_scangle_other 2.672 r_scbond_it 1.928 r_scbond_other 1.922 r_angle_refined_deg 1.882 r_mcangle_other 1.866 r_mcangle_it 1.862 r_angle_other_deg 1.534 r_mcbond_it 1.21 r_mcbond_other 1.195 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1146 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing