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Coxsackievirus B3 3C protease in C121 spacegroup
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 ShotGun1 Eco
0.2 Magnesium chloride hexahydrate
0.1 M Tris, pH 8.5
30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.23 44.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.503 α = 90 b = 64.871 β = 115.874 c = 39.43 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 9M 2023-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.34 47.78 66.32 0.992 29.2 5.6 26456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.36 0.648
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.34 47.778 26456 1314 66.317 0.157 0.1545 0.1551 0.2029 0.2039 24.327
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] -1.466 0.191 -0.112 0.947
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.73 r_lrange_other 19.592 r_scangle_it 15.891 r_scangle_other 15.884 r_dihedral_angle_3_deg 14.667 r_dihedral_angle_6_deg 14.662 r_mcangle_other 12.474 r_mcangle_it 12.472 r_dihedral_angle_2_deg 11.9 r_scbond_it 11.585
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.73 r_lrange_other 19.592 r_scangle_it 15.891 r_scangle_other 15.884 r_dihedral_angle_3_deg 14.667 r_dihedral_angle_6_deg 14.662 r_mcangle_other 12.474 r_mcangle_it 12.472 r_dihedral_angle_2_deg 11.9 r_scbond_it 11.585 r_scbond_other 11.578 r_mcbond_it 9.034 r_mcbond_other 9.026 r_dihedral_angle_1_deg 7.225 r_rigid_bond_restr 5.99 r_angle_refined_deg 2.199 r_angle_other_deg 0.894 r_nbd_refined 0.212 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.169 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.123 r_symmetry_nbd_refined 0.109 r_symmetry_nbtor_other 0.082 r_chiral_restr_other 0.016 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1393 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing