7M6H

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG7-20


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.304
f_angle_d1.047
f_chiral_restr0.068
f_plane_restr0.008
f_bond_d0.006
Sample
Ternary complex of BG7-20 Fab bound to SARS-CoV-2 spike trimer
Sample Components
SARS-CoV-2 spike trimer
BG7-20 Fab
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3s blot, 0 blot force
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles135666
Reported Resolution (Å)4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6XKL)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI ARCTICA
Minimum Defocus (nm)700
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification45000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEMv3.8
CTF CORRECTIONcryoSPARC2.14
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTPHENIX1.19
INITIAL EULER ASSIGNMENTcryoSPARC2.14
FINAL EULER ASSIGNMENTcryoSPARC2.14
CLASSIFICATIONcryoSPARC2.14
RECONSTRUCTIONcryoSPARC2.14
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION809834Blob picker