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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 Z54615640 (A71EV2A-x0354)
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 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.149 α = 90 b = 56.216 β = 95.34 c = 32.396 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 2023-10-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.94055 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 1.09 47.02 87.7 0.116 0.125 0.047 0.998 13.7 7.1 56084
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 1.09 1.11 42.3 3.72 4.051 1.577 0.249 6.1
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 1.09 47.02 53163 2736 87.2 0.18195 0.18123 0.1921 0.19518 0.2042 RANDOM 14.817
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] 0.07 -0.34 0.07 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.718 r_dihedral_angle_4_deg 23.841 r_dihedral_angle_3_deg 12.919 r_dihedral_angle_1_deg 6.998 r_long_range_B_refined 4.806 r_long_range_B_other 4.805 r_scangle_other 2.983 r_angle_other_deg 2.484 r_scbond_it 2.038 r_scbond_other 2.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.718 r_dihedral_angle_4_deg 23.841 r_dihedral_angle_3_deg 12.919 r_dihedral_angle_1_deg 6.998 r_long_range_B_refined 4.806 r_long_range_B_other 4.805 r_scangle_other 2.983 r_angle_other_deg 2.484 r_scbond_it 2.038 r_scbond_other 2.037 r_angle_refined_deg 1.973 r_mcangle_other 1.886 r_mcangle_it 1.87 r_mcbond_other 1.225 r_mcbond_it 1.223 r_chiral_restr 0.097 r_bond_other_d 0.035 r_gen_planes_other 0.021 r_bond_refined_d 0.016 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 236 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction