Local refinement of Fab-14/SARS-CoV-2 D614G spike complex, Mode IV, Subgroup I conformation

entry_id	9ynx
deposition_date	2025-10-12
title	Local refinement of Fab-14/SARS-CoV-2 D614G spike complex, Mode IV, Subgroup I conformation
keywords	SARS-CoV-2, neutraling antibody, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	45.23 Å
rg_electron	45.17 Å
i0	289936000.00
molecular_weight	138200.0 kDa
excluded_volume	172150 ų
envelope_volume	256410 ų
shell_volume	49200 ų
envelope_diameter	148.6 Å
shell_rg	47.59 Å
envelope_rg	43.60 Å
shape_rg	45.13 Å
total_rg	45.45 Å
total_atoms	9742
n_residues	1266
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	144.3 Å
rg_real	45.19 Å
rg_real_error	1.30 Å
i0_real	2.8990e+08
i0_real_error	5.8230e+06
rg_reciprocal	45.23 Å
i0_reciprocal	289900000.0000
total_estimate	0.8761
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.9 Å
skewness	0.150
kurtosis	-0.586
angular_range	— – 0.1750 Å−1
current_alpha	0.0000
highest_alpha	12910000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.637

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	4.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	4.10 Å
resolution_method	—
num_particles	66402

Files (7)

• pr_distribution /app/data/pr_computation/yn/9ynx/pr_distribution.json
• pr_output /app/data/pr_computation/yn/9ynx/9ynx.pr.out
• pr_plot /app/data/visualization/pr_computation/yn/9ynx/9ynx_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/yn/9ynx/9ynx.dat
• saxs_fit /app/data/saxs_computation/yn/9ynx/9ynx.fit
• saxs_log /app/data/saxs_computation/yn/9ynx/9ynx.log
• saxs_plot /app/data/visualization/saxs_computation/yn/9ynx/9ynx_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/yn/9ynx/9ynx.fit
pddf	/app/data/pr_computation/yn/9ynx/9ynx.pr.out
profile	/app/data/saxs_computation/yn/9ynx/9ynx.dat