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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-0031972-001 (A71EV2A-x3223)
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 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.733 α = 90 b = 57.149 β = 94.64 c = 64.871 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 2024-10-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92208 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 1.23 64.66 87.7 0.064 0.07 0.028 0.998 16 5.6 80442
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 1.23 1.25 36.3 0.922 1.227 0.799 0.384 2
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 1.23 64.66 76524 3860 87.69 0.18998 0.18916 0.2028 0.20573 0.2163 RANDOM 16.713
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] -0.21 0.37 0.25 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.025 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 12.914 r_dihedral_angle_1_deg 6.677 r_long_range_B_other 6.14 r_long_range_B_refined 6.085 r_scangle_other 3.33 r_scbond_it 2.265 r_scbond_other 2.264 r_mcangle_it 2.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.025 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 12.914 r_dihedral_angle_1_deg 6.677 r_long_range_B_other 6.14 r_long_range_B_refined 6.085 r_scangle_other 3.33 r_scbond_it 2.265 r_scbond_other 2.264 r_mcangle_it 2.155 r_mcangle_other 2.155 r_angle_refined_deg 1.776 r_angle_other_deg 1.449 r_mcbond_other 1.302 r_mcbond_it 1.212 r_chiral_restr 0.088 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.003 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 2166 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction