Crystal structure of SARS-CoV-2 RBD in complex with human Ab401 Fab

entry_id	9zdu
deposition_date	2025-11-26
title	Crystal structure of SARS-CoV-2 RBD in complex with human Ab401 Fab
keywords	neutralizing antibody, viral protein, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
method	X-RAY DIFFRACTION

rg_guinier	30.77 Å
rg_electron	30.41 Å
i0	81252100.00
molecular_weight	70557.0 kDa
excluded_volume	87871 ų
envelope_volume	113230 ų
shell_volume	32467 ų
envelope_diameter	111.0 Å
shell_rg	36.25 Å
envelope_rg	30.14 Å
shape_rg	30.36 Å
total_rg	31.08 Å
total_atoms	4972
n_residues	623
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	103.0 Å
rg_real	30.92 Å
rg_real_error	0.90 Å
i0_real	8.1250e+07
i0_real_error	1.2240e+06
rg_reciprocal	30.86 Å
i0_reciprocal	81250000.0000
total_estimate	0.8731
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.3 Å
skewness	0.463
kurtosis	-0.272
angular_range	— – 0.2550 Å−1
current_alpha	0.0000
highest_alpha	9644000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.854

Unit Cell

length_a	83.612 Å
length_b	83.612 Å
length_c	217.706 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

Symmetry

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

Refinement

resolution	2.600 Å
resolution_low	45.840 Å
r_factor	0.2219
r_work	0.2191
r_free	0.2530

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/zd/9zdu/pr_distribution.json
• pr_output /app/data/pr_computation/zd/9zdu/9zdu.pr.out
• pr_plot /app/data/visualization/pr_computation/zd/9zdu/9zdu_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/zd/9zdu/9zdu.dat
• saxs_fit /app/data/saxs_computation/zd/9zdu/9zdu.fit
• saxs_log /app/data/saxs_computation/zd/9zdu/9zdu.log
• saxs_plot /app/data/visualization/saxs_computation/zd/9zdu/9zdu_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/zd/9zdu/9zdu.fit
pddf	/app/data/pr_computation/zd/9zdu/9zdu.pr.out
profile	/app/data/saxs_computation/zd/9zdu/9zdu.dat