8VD7
MicroED structure of SARS-CoV-2 main protease (MPro/3CLPro) with missing cone eliminated by suspended drop
ELECTRON CRYSTALLOGRAPHY
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 | |
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Space Group | C 1 2 1 |
Data Collection
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | 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 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Sample |
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SARS-CoV-2 main protease (Mpro) |
Specimen Preparation | |
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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 |