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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 Z55993012 (A71EV2A-x0863)
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 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.779 α = 90 b = 61.165 β = 92.74 c = 32.377 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 2023-12-03 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 1.6 27 98 0.169 0.182 0.068 0.996 6.8 7 18388
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 1.6 1.63 96.1 2.103 2.265 0.837 0.356 7.2
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 1.6 27.01 17526 846 97.7 0.20353 0.20175 0.2116 0.24527 0.2393 RANDOM 29.441
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] -0.41 -0.49 1.01 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.858 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 16.642 r_long_range_B_other 10.246 r_long_range_B_refined 10.224 r_dihedral_angle_1_deg 6.899 r_scangle_other 3.475 r_mcangle_it 3.456 r_mcangle_other 3.447 r_scbond_it 2.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.858 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 16.642 r_long_range_B_other 10.246 r_long_range_B_refined 10.224 r_dihedral_angle_1_deg 6.899 r_scangle_other 3.475 r_mcangle_it 3.456 r_mcangle_other 3.447 r_scbond_it 2.189 r_scbond_other 2.175 r_mcbond_other 1.922 r_mcbond_it 1.854 r_angle_refined_deg 1.577 r_angle_other_deg 1.3 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 1083 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction