7Z9Q

CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 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
r_dihedral_angle_2_deg	29.835
r_lrange_it	17.501
r_lrange_other	17.501
r_dihedral_angle_4_deg	15.466
r_dihedral_angle_3_deg	13.488
r_mcangle_it	7.486
r_mcangle_other	7.485
r_scangle_it	7.406
r_scangle_other	7.406
r_dihedral_angle_1_deg	6.354
r_mcbond_it	4.245
r_mcbond_other	4.245
r_scbond_it	4.011
r_scbond_other	4.011
r_angle_other_deg	1.544
r_angle_refined_deg	1.469
r_nbd_refined	0.206
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.16
r_ncsr_local_group_2	0.103
r_ncsr_local_group_1	0.101
r_chiral_restr	0.099
r_ncsr_local_group_3	0.087
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.068
r_bond_other_d	0.031
r_ext_dist_refined_d	0.031
r_ncsr_local_group_4	0.021
r_ncsr_local_group_5	0.021
r_ncsr_local_group_6	0.021
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.003

Sample
Complex between Spike and nanobody H11-A10
Sample Components
Spike glycoprotein trimer
Nanobody H11-A10

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 260 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 80% relative humidity and ambient temperature.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	305820
Reported Resolution (Å)	3.6
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)	51.5

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1500
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
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
MODEL REFINEMENT	REFMAC
INITIAL EULER ASSIGNMENT	RELION	3.08
FINAL EULER ASSIGNMENT	RELION	3.08
CLASSIFICATION	RELION	3.08
RECONSTRUCTION	RELION	3.08

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3264123