Cryo-EM structure of SARS-CoV-2 WT spike protein in complex with nAb 1C4

entry_id	9w14
deposition_date	2025-07-25
title	Cryo-EM structure of SARS-CoV-2 WT spike protein in complex with nAb 1C4
keywords	SARS-CoV-2, Neutralizing antibody, Cryo-EM, Viral protein/Immune system, Viral protein-immune system complex, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	24.53 Å
rg_electron	23.70 Å
i0	33759200.00
molecular_weight	44716.0 kDa
excluded_volume	55868 ų
envelope_volume	68691 ų
shell_volume	24713 ų
envelope_diameter	88.3 Å
shell_rg	30.22 Å
envelope_rg	23.92 Å
shape_rg	23.65 Å
total_rg	24.65 Å
total_atoms	3161
n_residues	412
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	85.3 Å
rg_real	24.49 Å
rg_real_error	0.75 Å
i0_real	3.3760e+07
i0_real_error	5.2420e+05
rg_reciprocal	24.50 Å
i0_reciprocal	33760000.0000
total_estimate	0.8736
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.4 Å
skewness	0.296
kurtosis	-0.407
angular_range	— – 0.3250 Å−1
current_alpha	0.0000
highest_alpha	8410000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.995

Unit Cell

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

Symmetry

space_group	P 1
int_tables_number	1
crystal_system	—

Refinement

resolution	2.330 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	2.33 Å
resolution_method	—
num_particles	91916

Files (7)

• pr_distribution /app/data/pr_computation/w1/9w14/pr_distribution.json
• pr_output /app/data/pr_computation/w1/9w14/9w14.pr.out
• pr_plot /app/data/visualization/pr_computation/w1/9w14/9w14_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/w1/9w14/9w14.dat
• saxs_fit /app/data/saxs_computation/w1/9w14/9w14.fit
• saxs_log /app/data/saxs_computation/w1/9w14/9w14.log
• saxs_plot /app/data/visualization/saxs_computation/w1/9w14/9w14_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/w1/9w14/9w14.fit
pddf	/app/data/pr_computation/w1/9w14/9w14.pr.out
profile	/app/data/saxs_computation/w1/9w14/9w14.dat