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Crystal structure of the SARS-CoV-2 Main Protease
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% DMSO, 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.76 α = 90 b = 53.98 β = 101.18 c = 114.35 γ = 90
Symmetry Space Group P 1 21 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 2020-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978564 SOLEIL PROXIMA 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 1.743 48.64 95 0.993 7.72 6.2 52176
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 1.743 1.85 69.2 0.509
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 1.743 43.949 52172 2609 95.01 0.21 0.2073 0.2049 0.2547 0.2531 29.063
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] 0.126 -1.221 0.311 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.565 r_dihedral_angle_4_deg 20.42 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_1_deg 7.834 r_lrange_other 6.356 r_lrange_it 6.354 r_scangle_it 4.362 r_scangle_other 4.362 r_mcangle_it 3.406 r_mcangle_other 3.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.565 r_dihedral_angle_4_deg 20.42 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_1_deg 7.834 r_lrange_other 6.356 r_lrange_it 6.354 r_scangle_it 4.362 r_scangle_other 4.362 r_mcangle_it 3.406 r_mcangle_other 3.406 r_scbond_it 2.782 r_scbond_other 2.781 r_mcbond_it 2.277 r_mcbond_other 2.277 r_angle_refined_deg 1.538 r_angle_other_deg 1.353 r_symmetry_xyhbond_nbd_refined 0.207 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_other 0.179 r_symmetry_nbd_refined 0.173 r_nbd_other 0.172 r_nbtor_refined 0.167 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4727 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling MOLREP phasing XDS data processing Coot model building