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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 Z1216861874 (A71EV2A-x0525)
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 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.088 α = 90 b = 56.539 β = 95.26 c = 32.421 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 2023-10-11 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 1.19 47.19 99.4 0.135 0.146 0.055 0.998 9.2 6.8 49334
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 1.19 1.21 98.9 2.732 2.965 1.137 0.369 6.7
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 1.19 47.2 46757 2406 99.02 0.17392 0.17311 0.179 0.18889 0.1936 RANDOM 16.172
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] -0.06 -0.42 0.41 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.521 r_dihedral_angle_4_deg 24.16 r_dihedral_angle_3_deg 12.561 r_dihedral_angle_1_deg 6.733 r_long_range_B_other 5.229 r_long_range_B_refined 5.221 r_scangle_other 3.187 r_angle_other_deg 2.44 r_scbond_it 2.271 r_scbond_other 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.521 r_dihedral_angle_4_deg 24.16 r_dihedral_angle_3_deg 12.561 r_dihedral_angle_1_deg 6.733 r_long_range_B_other 5.229 r_long_range_B_refined 5.221 r_scangle_other 3.187 r_angle_other_deg 2.44 r_scbond_it 2.271 r_scbond_other 2.27 r_mcangle_other 2.134 r_mcangle_it 2.123 r_angle_refined_deg 2.065 r_mcbond_other 1.404 r_mcbond_it 1.399 r_chiral_restr 0.112 r_bond_other_d 0.036 r_gen_planes_other 0.021 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 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 237 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction