☰ Navigation Tabs
The crystal structure of SARS-CoV-2 3C-like protease in complex with a traditional Chinese Medicine Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 100 mM MES, pH6, 12% PEG 6000, 0.5% DMSO
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.178 α = 90 b = 81.411 β = 96.14 c = 91.218 γ = 90
Symmetry Space Group I 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 CCD OXFORD ONYX CCD 2021-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 24.499 99.7 0.129 0.991 10.5 4.4 22123
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 2.1 2.18 0.814
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6LU7 2.1 24.499 22123 1133 99.563 0.217 0.2159 0.2422 0.2441 31.129
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] 0.025 0.001 -0.009 -0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.754 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_4_deg 7.348 r_dihedral_angle_1_deg 6.781 r_lrange_other 4.206 r_lrange_it 4.179 r_angle_other_deg 2.361 r_mcangle_it 2.09 r_mcangle_other 2.089 r_scangle_it 1.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.754 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_4_deg 7.348 r_dihedral_angle_1_deg 6.781 r_lrange_other 4.206 r_lrange_it 4.179 r_angle_other_deg 2.361 r_mcangle_it 2.09 r_mcangle_other 2.089 r_scangle_it 1.664 r_scangle_other 1.663 r_angle_refined_deg 1.22 r_mcbond_it 1.166 r_mcbond_other 1.165 r_scbond_it 0.975 r_scbond_other 0.974 r_symmetry_nbd_other 0.221 r_nbd_refined 0.211 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.143 r_nbd_other 0.134 r_xyhbond_nbd_refined 0.11 r_symmetry_nbd_refined 0.081 r_symmetry_nbtor_other 0.065 r_chiral_restr 0.048 r_bond_other_d 0.036 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_refined_d 0.002 r_symmetry_xyhbond_nbd_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2295 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing