7M6H | pdb_00007m6h

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

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.304
f_angle_d	1.047
f_chiral_restr	0.068
f_plane_restr	0.008
f_bond_d	0.006

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 State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3s blot, 0 blot force

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	135666
Reported Resolution (Å)	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 (6XKL)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI ARCTICA
Minimum Defocus (nm)	700
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	45000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM	v3.8
CTF CORRECTION	cryoSPARC	2.14
MODEL FITTING	UCSF Chimera
MODEL REFINEMENT	PHENIX	1.19
INITIAL EULER ASSIGNMENT	cryoSPARC	2.14
FINAL EULER ASSIGNMENT	cryoSPARC	2.14
CLASSIFICATION	cryoSPARC	2.14
RECONSTRUCTION	cryoSPARC	2.14

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		809834	Blob picker