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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-0030497-001 (A71EV2A-x2339)
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 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.158 α = 90 b = 57.664 β = 92.26 c = 32.736 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 2024-09-05 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 1.66 48.23 99.9 0.072 0.078 0.03 0.998 14 6.9 19414
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 1.66 1.69 99.8 2.542 2.742 1.021 0.374 7.1
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 (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 1.66 48.25 18423 977 99.73 0.19184 0.18811 0.2475 0.2599 0.2803 RANDOM 42.383
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] -0.22 2.49 -0.9 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.589 r_dihedral_angle_4_deg 20.321 r_dihedral_angle_3_deg 15.439 r_long_range_B_refined 11.024 r_long_range_B_other 11.022 r_dihedral_angle_1_deg 6.776 r_scangle_other 4.29 r_mcangle_it 4.045 r_mcangle_other 4.044 r_scbond_it 3.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.589 r_dihedral_angle_4_deg 20.321 r_dihedral_angle_3_deg 15.439 r_long_range_B_refined 11.024 r_long_range_B_other 11.022 r_dihedral_angle_1_deg 6.776 r_scangle_other 4.29 r_mcangle_it 4.045 r_mcangle_other 4.044 r_scbond_it 3.021 r_scbond_other 2.979 r_mcbond_other 2.581 r_mcbond_it 2.484 r_angle_refined_deg 1.479 r_angle_other_deg 1.293 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 1074 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction