7UZ4

Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-3


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7SC1 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.553
f_angle_d0.529
f_chiral_restr0.045
f_bond_d0.005
f_plane_restr0.004
Sample
SARS-CoV-2 S 6P in complex with M8a-3 Fab
Sample Components
Severe acute respiratory syndrome coronavirus 2 spike glycoprotein
M8a-3 Fab VH and VL domains
M8a-3 Fab CH1 and CL domains
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles272779
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7SC1)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value90
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC3.2
MODEL FITTINGUCSF Chimera1.16
INITIAL EULER ASSIGNMENTcryoSPARC3.2
FINAL EULER ASSIGNMENTcryoSPARC3.2
CLASSIFICATIONcryoSPARC3.2
RECONSTRUCTIONcryoSPARC3.2
MODEL REFINEMENTPHENIX1.19.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1026209