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9wlb

Local refinement region of SARS-CoV-2 spike RBD in complex with antibodies S309 and CT1-1.

Method: ELECTRON MICROSCOPY D_max: 111.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wlb
deposition_date	2025-09-02
title	Local refinement region of SARS-CoV-2 spike RBD in complex with antibodies S309 and CT1-1.
keywords	SARS-CoV-2, RBD, Fab, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.81 Å
rg_electron	32.73 Å
i0	68236100.00
molecular_weight	64556.0 kDa
excluded_volume	80096 Å³
envelope_volume	106730 Å³
shell_volume	28950 Å³
envelope_diameter	117.5 Å
shell_rg	37.03 Å
envelope_rg	32.82 Å
shape_rg	32.72 Å
total_rg	33.15 Å
total_atoms	4569
n_residues	643
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

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3. P(r) Analysis (GNOM)

dmax	111.5 Å
rg_real	33.13 Å
rg_real_error	1.17 Å
i0_real	6.8240e+07
i0_real_error	1.2260e+06
rg_reciprocal	33.00 Å
i0_reciprocal	68230000.0000
total_estimate	0.8340
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.448
kurtosis	-0.541
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	12300000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.662; Smooth: 0.872

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	S309 Fab light chain
formula_weight	23204.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	4569

EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	S309 Fab heavy chain
formula_weight	13918.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQGTLVTVS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	CT1-1 Fab heavy chain
formula_weight	13448.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QMQLVQSGPEVKKPGTSVKVSCKASGFTFTSAAVQWVRQARGQRLEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSGGSCHDGFDIWGQGTMVTVSS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Spike protein S1
formula_weight	25122.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF

Source

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

Entity 5 polymer

description	CT1-1 Fab light chain
formula_weight	11786.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVLTQTPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYVGLTGWTFGQGTKVEIK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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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	—

resolution	3.740 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.74 Å
resolution_method	—
num_particles	56564

fit	/app/data/saxs_computation/wl/9wlb/9wlb.fit
pddf	/app/data/pr_computation/wl/9wlb/9wlb.pr.out
profile	/app/data/saxs_computation/wl/9wlb/9wlb.dat

Local refinement region of SARS-CoV-2 spike RBD in complex with antibodies S309 and CT1-1.

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

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)