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MicroED structure of SARS-CoV-2 main protease (MPro/3CLPro) with missing cone eliminated by suspended drop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.54 α = 90 b = 55.53 β = 101.074 c = 45.37 γ = 90
Symmetry Space Group C 1 2 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT FREE R-VALUE 2.15 44.525 14817 742 95.52 0.213 0.2116 0.2484 44.804
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] 4.983 0.184 -0.578 -4.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.815 r_dihedral_angle_6_deg 15.072 r_dihedral_angle_2_deg 10.714 r_lrange_it 9.531 r_lrange_other 9.529 r_dihedral_angle_1_deg 7.265 r_scangle_it 7.257 r_scangle_other 7.255 r_mcangle_it 5.602 r_mcangle_other 5.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.815 r_dihedral_angle_6_deg 15.072 r_dihedral_angle_2_deg 10.714 r_lrange_it 9.531 r_lrange_other 9.529 r_dihedral_angle_1_deg 7.265 r_scangle_it 7.257 r_scangle_other 7.255 r_mcangle_it 5.602 r_mcangle_other 5.6 r_scbond_it 4.665 r_scbond_other 4.663 r_mcbond_it 3.814 r_mcbond_other 3.814 r_angle_refined_deg 1.744 r_angle_other_deg 0.598 r_nbd_refined 0.239 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.185 r_nbd_other 0.183 r_symmetry_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d
Software Software Software Name Purpose REFMAC refinement
Sample SARS-CoV-2 main protease (Mpro)
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 2.15 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 115.54 Length b 55.53 Length c 55.53 Angle Alpha 90 Angle Beta 101.074 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol OTHER Refinement Target Rwork/Rfree gap of less than 5% Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 0.0025
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING Coot MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE