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Group deposition for crystallographic fragment screening of Coxsackievirus A16 (G-10) 2A protease -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with Z362020366 (A71EV2A-x1293)
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 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.116 α = 90 b = 56.531 β = 94.58 c = 64.524 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 16M 2024-02-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.94054 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 1.12 42.92 97.6 0.068 0.073 0.028 0.999 11.3 6.7 115137
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 1.12 1.18 87.7 1.524 1.689 0.712 0.453 5.3
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 1.12 42.96 109656 5317 97.34 0.17939 0.1785 0.1822 0.19732 0.2015 RANDOM 16.101
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] 0.09 0.43 -0.14 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.71 r_dihedral_angle_4_deg 22.267 r_dihedral_angle_3_deg 11.872 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 6.03 r_long_range_B_other 5.66 r_scangle_other 3.456 r_scbond_it 2.49 r_scbond_other 2.485 r_mcangle_it 2.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.71 r_dihedral_angle_4_deg 22.267 r_dihedral_angle_3_deg 11.872 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 6.03 r_long_range_B_other 5.66 r_scangle_other 3.456 r_scbond_it 2.49 r_scbond_other 2.485 r_mcangle_it 2.019 r_mcangle_other 2.018 r_angle_refined_deg 1.782 r_angle_other_deg 1.555 r_mcbond_it 1.33 r_mcbond_other 1.33 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 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 366 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction