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Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 0.12 M Ethylene glycols (0.3 M Diethylene glycol, 0.3 M Triethylene glycol, 0.3 M Tetraethylene glycol, 0.3 M Pentaethylene glycol), 0.1 M buffer system 2 (1.0 M Sodium HEPES, MOPS (acid), pH 7.5), pH 7.5, 30% Precipitant mix 3 (20% glycerol, 10% PEG 4000)
Crystal Properties Matthews coefficient Solvent content 2.11 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.083 α = 90 b = 104.083 β = 90 c = 91.246 γ = 120
Symmetry Space Group P 61 2 2
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 PILATUS3 S 6M 2020-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.7 45.62 100 0.074 0.075 0.012 1 32.4 38.5 32640
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 1.7 1.79 100 1.574 1.595 0.257 0.861 38
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 6Y2E 1.7 45.247 32594 1625 99.982 0.195 0.192 0.2003 0.2434 0.2515 32.48
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] -0.334 -0.167 -0.334 1.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.738 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_3_deg 13.75 r_dihedral_angle_1_deg 7.513 r_lrange_it 6.893 r_lrange_other 6.828 r_scangle_it 5.148 r_scangle_other 5.147 r_mcangle_it 3.919 r_mcangle_other 3.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.738 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_3_deg 13.75 r_dihedral_angle_1_deg 7.513 r_lrange_it 6.893 r_lrange_other 6.828 r_scangle_it 5.148 r_scangle_other 5.147 r_mcangle_it 3.919 r_mcangle_other 3.918 r_scbond_it 3.548 r_scbond_other 3.416 r_mcbond_it 2.881 r_mcbond_other 2.881 r_angle_refined_deg 1.814 r_angle_other_deg 1.442 r_dihedral_angle_other_3_deg 1.398 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.204 r_xyhbond_nbd_refined 0.202 r_nbd_other 0.202 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.172 r_metal_ion_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.129 r_chiral_restr 0.088 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing