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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 Z53860899 (A71EV2A-x0351)
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 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.601 α = 90 b = 60.716 β = 93.33 c = 32.38 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 1.36 46.55 99.3 0.12 0.131 0.05 0.996 9.8 6.9 29945
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 1.36 1.38 98.1 2.606 2.837 1.105 0.263 6.3
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 1.36 46.54 28390 1403 98.64 0.22405 0.22238 0.2306 0.26167 0.2649 RANDOM 26.852
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] 0.29 -0.34 0.05 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.712 r_dihedral_angle_4_deg 16.495 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 6.953 r_long_range_B_other 5.736 r_long_range_B_refined 5.671 r_scangle_other 2.752 r_mcangle_it 2.674 r_mcangle_other 2.623 r_scbond_other 1.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.712 r_dihedral_angle_4_deg 16.495 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 6.953 r_long_range_B_other 5.736 r_long_range_B_refined 5.671 r_scangle_other 2.752 r_mcangle_it 2.674 r_mcangle_other 2.623 r_scbond_other 1.695 r_scbond_it 1.69 r_mcbond_other 1.452 r_angle_refined_deg 1.417 r_mcbond_it 1.401 r_angle_other_deg 1.295 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 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 1074 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction