7TOZ
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D7 state
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7KDK |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.941 |
f_angle_d | 1.825 |
f_chiral_restr | 0.1 |
f_plane_restr | 0.018 |
f_bond_d | 0.013 |
Sample |
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Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D7 state |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 55198 |
Reported Resolution (Å) | 4.07 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 (7KDK) | ||||
Refinement Space | |||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 55 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 750 |
Maximum Defocus (nm) | 2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | Coot | |
MODEL FITTING | UCSF ChimeraX | |
MODEL REFINEMENT | ISOLDE | |
MODEL REFINEMENT | UCSF ChimeraX | |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |