SAXSdb — 9zt6

▼

1. Structure Basics

entry_id	9zt6
deposition_date	2025-12-23
title	SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor8
keywords	SARS-CoV-2, Coronavirus, Immune system, antibody, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	37.25 Å
rg_electron	36.35 Å
i0	374331000.00
molecular_weight	155350.0 kDa
excluded_volume	193560 Å³
envelope_volume	249570 Å³
shell_volume	56281 Å³
envelope_diameter	139.7 Å
shell_rg	43.08 Å
envelope_rg	36.84 Å
shape_rg	36.40 Å
total_rg	36.60 Å
total_atoms	10928
n_residues	1445
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	128.4 Å
rg_real	37.34 Å
rg_real_error	1.10 Å
i0_real	3.7430e+08
i0_real_error	6.3960e+06
rg_reciprocal	37.29 Å
i0_reciprocal	374300000.0000
total_estimate	0.8668
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	42.8 Å
skewness	0.453
kurtosis	-0.193
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	83840000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.934

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Human polyclonal Fab model with polyalanine backbone - Heavy chain
formula_weight	10181.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10928

XXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXXXXXXXXX

Entity 2 polymer

description	Human polyclonal Fab model with polyalanine backbone - Light chain
formula_weight	8990.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

XXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXXXX

Entity 3 polymer

description	Spike protein S2
formula_weight	52342.1 kDa
mutation	S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,D,E

SLGAENCVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLACTITSGWTCGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNFLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSGSHHHHHHHH

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	7

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	10

▶

6. Citations (1)

▶

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	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.83 Å
resolution_method	—
num_particles	189213

fit	/app/data/saxs_computation/zt/9zt6/9zt6.fit
pddf	/app/data/pr_computation/zt/9zt6/9zt6.pr.out
profile	/app/data/saxs_computation/zt/9zt6/9zt6.dat

SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor8

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)