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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 2.47 50.24
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 0.17084 0.16996 0.178 0.18712 0.1942 RANDOM 16.338
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 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_4_deg 24.215 r_dihedral_angle_3_deg 12.351 r_dihedral_angle_1_deg 6.86 r_long_range_B_refined 6.461 r_long_range_B_other 6.458 r_scangle_other 3.02 r_mcangle_other 2.132 r_mcangle_it 2.125 r_scbond_it 2.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_4_deg 24.215 r_dihedral_angle_3_deg 12.351 r_dihedral_angle_1_deg 6.86 r_long_range_B_refined 6.461 r_long_range_B_other 6.458 r_scangle_other 3.02 r_mcangle_other 2.132 r_mcangle_it 2.125 r_scbond_it 2.096 r_scbond_other 2.068 r_angle_refined_deg 1.81 r_angle_other_deg 1.508 r_mcbond_other 1.36 r_mcbond_it 1.345 r_chiral_restr 0.091 r_bond_refined_d 0.013 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 1083 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction XDS data reduction