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Group deposition of Coxsackievirus A16 (G-10) 2A protease in complex with inhibitors from the ASAP AViDD centre -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with ASAP-0030968-001 (A71EV2A-x2513)
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 6.05 293.15 0.1 M MES, pH 6.05, 16 % PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.369 α = 90 b = 57.653 β = 91.87 c = 32.833 γ = 90
Symmetry Space Group C 1 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 EIGER2 XE 9M 2024-09-06 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92134 Diamond I04-1
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 1.54 48.26 97.9 0.049 0.053 0.02 0.998 21.2 6.9 23889
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 1.54 1.57 95.1 1.568 1.724 0.703 0.57 5.8
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 1.54 48.28 22667 1220 97.64 0.19987 0.1968 0.2478 0.25717 0.2748 RANDOM 31.882
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] 0.39 0.29 -0.11 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.907 r_dihedral_angle_4_deg 21.134 r_dihedral_angle_3_deg 13.222 r_long_range_B_refined 10.163 r_long_range_B_other 10.161 r_dihedral_angle_1_deg 7.488 r_scangle_other 3.671 r_mcangle_it 3.174 r_mcangle_other 3.173 r_scbond_it 2.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.907 r_dihedral_angle_4_deg 21.134 r_dihedral_angle_3_deg 13.222 r_long_range_B_refined 10.163 r_long_range_B_other 10.161 r_dihedral_angle_1_deg 7.488 r_scangle_other 3.671 r_mcangle_it 3.174 r_mcangle_other 3.173 r_scbond_it 2.179 r_scbond_other 2.169 r_mcbond_other 1.793 r_mcbond_it 1.737 r_angle_refined_deg 1.546 r_angle_other_deg 1.332 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 1083 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction