7Z7X | pdb_00007z7x

CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H6 nanobody complex

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.5069
f_angle_d	0.6022
f_chiral_restr	0.047
f_bond_d	0.006
f_plane_restr	0.004

Sample
Complex between Spike and nanobody H11-H6
Sample Components
Spike glycoprotein trimer with fibritin tag
Nanobody H11-H6

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	SPOTITON
Cryogen Name	ETHANE
Sample Vitrification Details	SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 120 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) or for 60-80 s, 12 mA (easiGlow, Pelco) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 79-81% relative humidity and ambient temperature.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	210571
Reported Resolution (Å)	3.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6ZHD, 6ZHD, 6ZHD)
Refinement Space	RECIPROCAL
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)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	EPU auto-function coma free correction

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.08
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	3.08
FINAL EULER ASSIGNMENT	RELION	3.08
CLASSIFICATION	RELION	3.08
RECONSTRUCTION	RELION	3.08
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1609112