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CRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE COMPLEXED WITH FRAGMENT F01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M NaFORMATE, 20% PEG 3350, 10%
GLYCEROL, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 2.01 38.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.17 α = 90 b = 53.56 β = 101.24 c = 44.88 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 EIGER X 9M 2021-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980111 SOLEIL PROXIMA 2
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 1.47 48.442 99.4 0.999 13.68 6.9 45078
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 1.47 1.56 0.645
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7K3T 1.474 48.442 45078 2254 99.396 0.183 0.1814 0.18 0.2157 0.2168 23.901
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] 0.628 -0.182 0.057 -0.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.865 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_4_deg 9.024 r_dihedral_angle_1_deg 7.464 r_angle_refined_deg 1.856 r_angle_other_deg 1.491 r_nbd_refined 0.228 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.182 r_nbd_other 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.865 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_4_deg 9.024 r_dihedral_angle_1_deg 7.464 r_angle_refined_deg 1.856 r_angle_other_deg 1.491 r_nbd_refined 0.228 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.182 r_nbd_other 0.182 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbd_refined 0.168 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2382 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing MxCuBE data collection