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9ssm

Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD

Method: X-RAY DIFFRACTION D_max: 111.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ssm
deposition_date	2025-09-26
title	Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD
keywords	Neutralizing antibody SARS-CoV-2 Beta variant, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
method	X-RAY DIFFRACTION

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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	31.84 Å
rg_electron	31.81 Å
i0	72138100.00
molecular_weight	65917.0 kDa
excluded_volume	81705 Å³
envelope_volume	106110 Å³
shell_volume	30278 Å³
envelope_diameter	114.6 Å
shell_rg	35.74 Å
envelope_rg	31.90 Å
shape_rg	31.77 Å
total_rg	32.26 Å
total_atoms	8948
n_residues	619
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	111.7 Å
rg_real	32.24 Å
rg_real_error	0.99 Å
i0_real	7.2140e+07
i0_real_error	1.2620e+06
rg_reciprocal	32.07 Å
i0_reciprocal	72130000.0000
total_estimate	0.8194
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	29.1 Å
skewness	0.604
kurtosis	-0.151
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	11010000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.694

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	084-7D Fab Heavy Chain
formula_weight	24397.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	9014

EVQLLESGGGLVQPGGSLRLSCAASGFSFSSYAMNWVRQAPGKGLEWVSAISGGGDNIYYADSVKGRFTISRDNYKNTLHLQMKSLRAEDTAVYYCAKDHPSWGSSFLNWGQGILVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDLEVLFQ

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	084-7D Fab Light Chain
formula_weight	23401.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGRAPKLLIYTASNLESGVPSRFSGSGSGTEFSLTISSLQPDDFATYYCQQYNSYSLTFGGGTRVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Spike glycoprotein
formula_weight	28143.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGGPGHHHHHHHHGGLNDIFEAQKIEWHE

Source

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

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	65

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6. Citations (1)

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length_a	81.450 Å
length_b	84.368 Å
length_c	126.239 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.700 Å
resolution_low	50.000 Å
r_factor	0.2249
r_work	0.2226
r_free	0.2690

fit	/app/data/saxs_computation/ss/9ssm/9ssm.fit
pddf	/app/data/pr_computation/ss/9ssm/9ssm.pr.out
profile	/app/data/saxs_computation/ss/9ssm/9ssm.dat

Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD

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

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)