;Crystal structure of a protein mimic of SARS-CoV-2 spike's HR1 domain in complex with two nanobodies bound to different epitopes ;

entry_id	9rn6
deposition_date	2025-06-19
last_revision	2026-01-21
title	;Crystal structure of a protein mimic of SARS-CoV-2 spike's HR1 domain in complex with two nanobodies bound to different epitopes ;
keywords	Neutralizing nanobodies; SARS-Cov-2; Spike S2 subunit, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	37.68 Å
rg_electron	38.35 Å
i0	41137800.00
molecular_weight	49748.0 kDa
excluded_volume	61700 ų
envelope_volume	87425 ų
shell_volume	21263 ų
envelope_diameter	135.9 Å
shell_rg	38.86 Å
envelope_rg	38.00 Å
shape_rg	38.39 Å
total_rg	38.24 Å
total_atoms	6959
n_residues	454
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	129.2 Å
rg_real	38.34 Å
rg_real_error	2.17 Å
i0_real	4.1140e+07
i0_real_error	8.3440e+05
rg_reciprocal	37.94 Å
i0_reciprocal	41120000.0000
total_estimate	0.6650
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	21.5 Å
skewness	0.427
kurtosis	-0.907
angular_range	— – 0.2100 Å−1
current_alpha	0.0000
highest_alpha	2392000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.224; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.137; Smooth: 0.835

Unit Cell

length_a	47.560 Å
length_b	67.340 Å
length_c	230.780 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

Symmetry

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

Refinement

resolution	2.400 Å
resolution_low	19.990 Å
r_factor	0.2474
r_work	0.2466
r_free	0.2631

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/rn/9rn6/pr_distribution.json
• pr_output /app/data/pr_computation/rn/9rn6/9rn6.pr.out
• pr_plot /app/data/visualization/pr_computation/rn/9rn6/9rn6_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/rn/9rn6/9rn6.dat
• saxs_fit /app/data/saxs_computation/rn/9rn6/9rn6.fit
• saxs_log /app/data/saxs_computation/rn/9rn6/9rn6.log
• saxs_plot /app/data/visualization/saxs_computation/rn/9rn6/9rn6_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/rn/9rn6/9rn6.fit
pddf	/app/data/pr_computation/rn/9rn6/9rn6.pr.out
profile	/app/data/saxs_computation/rn/9rn6/9rn6.dat