Crystal structure of the walnut allergen Jug r 2 bound to the human-derived Fab 6D12

entry_id	9q1l
deposition_date	2025-08-14
last_revision	2026-01-21
title	Crystal structure of the walnut allergen Jug r 2 bound to the human-derived Fab 6D12
keywords	walnut, allergen, antibody binding, Fab, vicilin, alpha-hairpinin domains, seed storage protein, ALLERGEN-IMMUNE SYSTEM complex; ALLERGEN/IMMUNE SYSTEM
method	X-RAY DIFFRACTION

rg_guinier	35.26 Å
rg_electron	34.33 Å
i0	168263000.00
molecular_weight	101080.0 kDa
excluded_volume	125320 ų
envelope_volume	165620 ų
shell_volume	41399 ų
envelope_diameter	133.5 Å
shell_rg	39.65 Å
envelope_rg	33.92 Å
shape_rg	34.31 Å
total_rg	34.79 Å
total_atoms	13865
n_residues	937
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	124.7 Å
rg_real	35.25 Å
rg_real_error	1.35 Å
i0_real	1.6830e+08
i0_real_error	3.0170e+06
rg_reciprocal	35.26 Å
i0_reciprocal	168300000.0000
total_estimate	0.8754
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.6 Å
skewness	0.282
kurtosis	-0.400
angular_range	— – 0.2250 Å−1
current_alpha	0.0000
highest_alpha	14620000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.946

Unit Cell

length_a	98.541 Å
length_b	49.508 Å
length_c	111.093 Å
angle_alpha	90.00 °
angle_beta	104.73 °
angle_gamma	90.00 °
z_pdb	4

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

Refinement

resolution	1.560 Å
resolution_low	42.410 Å
r_factor	0.1679
r_work	0.1675
r_free	0.1954

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/q1/9q1l/pr_distribution.json
• pr_output /app/data/pr_computation/q1/9q1l/9q1l.pr.out
• pr_plot /app/data/visualization/pr_computation/q1/9q1l/9q1l_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/q1/9q1l/9q1l.dat
• saxs_fit /app/data/saxs_computation/q1/9q1l/9q1l.fit
• saxs_log /app/data/saxs_computation/q1/9q1l/9q1l.log
• saxs_plot /app/data/visualization/saxs_computation/q1/9q1l/9q1l_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/q1/9q1l/9q1l.fit
pddf	/app/data/pr_computation/q1/9q1l/9q1l.pr.out
profile	/app/data/saxs_computation/q1/9q1l/9q1l.dat