7X8Z

The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab188


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CCK 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.8217
f_angle_d0.517
f_chiral_restr0.0421
f_plane_restr0.0045
f_bond_d0.0026
Sample
The SARS-CoV-2 spike protein bound with the Fab fragment of a human neutralizing antibody Ab354
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles69153
Reported Resolution (Å)4.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (5CCK)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetCorelation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
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
PARTICLE SELECTIONcrYOLO
IMAGE ACQUISITIONEPU2.9
CTF CORRECTIONCTFFIND4
MODEL FITTINGCoot0.9.6
MODEL REFINEMENTPHENIX1.19.2-4158
INITIAL EULER ASSIGNMENTRELION3.1.2
FINAL EULER ASSIGNMENTRELION3.1.2
CLASSIFICATIONRELION3.1.2
RECONSTRUCTIONRELION3.1.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION