7R4I | pdb_00007r4i

The SARS-CoV-2 spike in complex with the 2.15 neutralizing nanobody

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.498
f_angle_d	0.731
f_chiral_restr	0.05
f_bond_d	0.016
f_plane_restr	0.007

Sample
The trimeric SARS-CooV-2 spike in complex with the 2.15 neutralizing nanobody
Sample Components
SARS-CoV-2 spike
Nanobody 2.15

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	40000
Reported Resolution (Å)	3.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (6ZXN, 6ZXN, 6ZXN, 6DBA, 6DBA)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	correlation coefficient
Overall B Value	140
Fitting Procedure
Details	Rigid body refinement. Real space refinement including 5 macro cycles of:Minimization_global, local_grid search and adp. Refinement at 4.0A of resolution. Refinement included NCS.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DARK FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera	1.15
MODEL FITTING	Coot	0.8.9.1
MODEL REFINEMENT	PHENIX	1.17.1_3660

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