7R40

Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7B62 
experimental modelPDB 7K4N 
experimental modelPDB 6M0J 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.896
f_angle_d0.713
f_chiral_restr0.051
f_plane_restr0.007
f_bond_d0.003
Sample
SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
Sample Components
SARS-CoV-2 spike glycoprotein
87G7 antibody Fab fragment
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles133550
Reported Resolution (Å)2.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC3
Map-Model Fitting and Refinement
Id1 (7B62, 7K4N, 7K4N, 6M0J)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)51.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONEPU2
MODEL FITTINGUCSF Chimera1.15.0
MODEL FITTINGCoot0.9.6
FINAL EULER ASSIGNMENTcryoSPARC
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.19.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION934811313636 particles were picked from 1331 images from 0.02% FOM dataset and 621175 particles were picked from 2500 images without FOM.