Co-crystal of broadly neutralizing VHH in complex with short neurotoxin 1 (P01426) Naja pallida

entry_id	9riu
deposition_date	2025-06-11
title	Co-crystal of broadly neutralizing VHH in complex with short neurotoxin 1 (P01426) Naja pallida
keywords	nanobody, VHH, antibody, toxin, snake toxin, snake venom, neutralizing; TOXIN
method	X-RAY DIFFRACTION

rg_guinier	24.59 Å
rg_electron	23.96 Å
i0	35931800.00
molecular_weight	41725.0 kDa
excluded_volume	50250 ų
envelope_volume	64361 ų
shell_volume	22943 ų
envelope_diameter	83.3 Å
shell_rg	30.29 Å
envelope_rg	23.84 Å
shape_rg	23.97 Å
total_rg	24.64 Å
total_atoms	5592
n_residues	376
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	81.4 Å
rg_real	24.58 Å
rg_real_error	0.52 Å
i0_real	3.5930e+07
i0_real_error	4.9110e+05
rg_reciprocal	24.58 Å
i0_reciprocal	35930000.0000
total_estimate	0.8976
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.4 Å
skewness	0.279
kurtosis	-0.485
angular_range	— – 0.3250 Å−1
current_alpha	0.0000
highest_alpha	4674000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.995

Unit Cell

length_a	104.150 Å
length_b	104.090 Å
length_c	79.340 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

Symmetry

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

Refinement

resolution	2.500 Å
resolution_low	23.290 Å
r_factor	0.3258
r_work	0.3238
r_free	0.3610

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/ri/9riu/pr_distribution.json
• pr_output /app/data/pr_computation/ri/9riu/9riu.pr.out
• pr_plot /app/data/visualization/pr_computation/ri/9riu/9riu_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/ri/9riu/9riu.dat
• saxs_fit /app/data/saxs_computation/ri/9riu/9riu.fit
• saxs_log /app/data/saxs_computation/ri/9riu/9riu.log
• saxs_plot /app/data/visualization/saxs_computation/ri/9riu/9riu_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/ri/9riu/9riu.fit
pddf	/app/data/pr_computation/ri/9riu/9riu.pr.out
profile	/app/data/saxs_computation/ri/9riu/9riu.dat