Experiment: 7YH6

Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M0J

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.1828
f_angle_d	0.6017
f_chiral_restr	0.0476
f_bond_d	0.0045
f_plane_restr	0.0036

Sample
SARS-COV-2 spike glycoprotein in complex with NIV-8
Sample Components
SARS-CoV-2 spike glycoprotein
NIV-8 Fab

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	blotting time 5 s and blotting force 5.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	64245
Reported Resolution (Å)	3.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6M0J)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	57

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.3.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	3.3.1
MODEL FITTING	UCSF Chimera	1.15
MODEL REFINEMENT	PHENIX	1.20
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.1
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.1
CLASSIFICATION	RELION	3.1.3
RECONSTRUCTION	cryoSPARC	3.3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		206354