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Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) at 1.2 A Resolution and a Possible Capture of Zinc Binding Intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 20% PEG 3350, 0.1 M MES pH 6.5, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 1.92 35.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.784 α = 90 b = 52.931 β = 100.07 c = 111.273 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 PIXEL DECTRIS EIGER X 16M 2020-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9793 NSLS-II 17-ID-2
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 1.2 27.39 97.8 0.094 0.103 0.042 0.997 11.6 6.2 78254
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 1.2 1.22 64.5 0.869 0.974 0.428 0.673 4.4
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 (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 6YB7 1.2 27.39 74325 3900 97.7 0.1367 0.1351 0.1383 0.1674 0.1692 RANDOM 16.705
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] -0.26 -0.02 0.22 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.193 r_dihedral_angle_3_deg 12.015 r_dihedral_angle_4_deg 10.102 r_dihedral_angle_1_deg 6.944 r_rigid_bond_restr 6.719 r_angle_refined_deg 2.206 r_angle_other_deg 1.694 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.193 r_dihedral_angle_3_deg 12.015 r_dihedral_angle_4_deg 10.102 r_dihedral_angle_1_deg 6.944 r_rigid_bond_restr 6.719 r_angle_refined_deg 2.206 r_angle_other_deg 1.694 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_gen_planes_other 0.01 r_bond_other_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing