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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 POB0140 (A71EV2A-x1247)
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 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.99 α = 90 b = 56.97 β = 92.55 c = 32.549 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 1.61 32.52 98.3 0.046 0.05 0.019 0.999 13.6 7.1 20676
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 1.61 1.69 97.9 2.81 3.027 1.119 0.451 7.1
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 1.61 32.54 19286 1040 96.41 0.19972 0.19613 0.2778 0.2651 0.3126 RANDOM 50.089
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] -0.34 3.45 -3.39 3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 16.569 r_long_range_B_refined 10.963 r_long_range_B_other 10.961 r_dihedral_angle_1_deg 6.53 r_mcangle_other 4.601 r_mcangle_it 4.6 r_scangle_other 4.587 r_scbond_it 3.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 16.569 r_long_range_B_refined 10.963 r_long_range_B_other 10.961 r_dihedral_angle_1_deg 6.53 r_mcangle_other 4.601 r_mcangle_it 4.6 r_scangle_other 4.587 r_scbond_it 3.125 r_scbond_other 3.109 r_mcbond_other 2.881 r_mcbond_it 2.752 r_angle_other_deg 2.518 r_angle_refined_deg 1.455 r_chiral_restr 0.067 r_bond_other_d 0.036 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 119 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction XDS data reduction