SAXSdb — 9w76

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1. Structure Basics

entry_id	9w76
deposition_date	2025-08-05
title	sarbecovirus Rc-o319 S-trimer in a locked-2 conformation
keywords	spike protein, VIRUS, VIRAL PROTEIN; VIRAL PROTEIN
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	48.60 Å
rg_electron	48.15 Å
i0	1983660000.00
molecular_weight	372440.0 kDa
excluded_volume	465880 Å³
envelope_volume	622710 Å³
shell_volume	104430 Å³
envelope_diameter	157.7 Å
shell_rg	54.61 Å
envelope_rg	47.56 Å
shape_rg	48.20 Å
total_rg	48.17 Å
total_atoms	26232
n_residues	3231
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	156.2 Å
rg_real	48.47 Å
rg_real_error	0.92 Å
i0_real	1.9840e+09
i0_real_error	3.3210e+07
rg_reciprocal	48.60 Å
i0_reciprocal	1984000000.0000
total_estimate	0.8657
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.6 Å
skewness	0.298
kurtosis	-0.397
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	312000000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.591

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Spike protein S1
formula_weight	138931.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	26232

MFILVLLNVLSVYGCVNITYGSHHLYVSSRTRGVYYPDDAFRSSTNVLHEGFFLPFDSNVTWYSFWNQKYSVATSPFGDGVYFSTIDKSNVVRGWVFGTTLDNDTQSVLLYNDGTHVRVEVCTFHFCPTPVFSASSPHLYSSAFNCTLNYTLASVRADFTEVDGSFKTIREFVFKLQDGSLNVYYASTSYVLAIGATSQLPSGVTPLVPLWKIPIGLNITNFKTLVYLRSDNTPLQAAYVVGHLKRRTMMFKYDENGTIVDAIDCALDPLSETKCTLRSFIVEKGIYQTSNFRVQPQDTVVRFPNITNLCPFSEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFQCYGVSSTKLNDLCFTNVYADSFVVRGDEVRQIAPGQTGVIADYNYKLPDDFTGCVLAWNSRNQDASTSGNFNYYYRIWRSEKLRPFERDIAHYDYQVGTQFKSSLKNYGFYSSAGDSHQPYRVVVLSFELLNAPATVCGPKQSTELIKNKCVNFNFNGLTGTGVLTDSNKKFQSFQQFGRDVSDFTDSVKDPKTLEVLDITPCSYGGVSVITPGTNASTQVAVLYQDVNCTDVPTAIHAEQLTPSWRVYSTGTNMFQTQAGCLIGAEHVNNSYDCDIPIGAGICATYHTPSMLRSANNNKRIVAYVMSLGAENSVAYSNNTIAIPTNFTISVTTEVMPVSMTKTSVDCTMYICGDSVECSTLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPDIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFVKQYGDCLGDIQARDLICAQKFNGLTVLPPLLTDEMIAAYTAALISGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQESLTSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDIISRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYIPSQERNFTTAPAICHEGKAHFPREGVFVSNGTHWFITQRNFYEPQIITTDNTFVSGTCDVVIGIVNNTVYDPLQPELESFKDELDKYFKNHTSPDIDLGDISGINASVVDIQKEIDILKDVAKNLNESLINLQELGKYEQYIKWPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEKSA

Source

organism	Sarbecovirus
ncbi_taxonomy_id	2509511
host_organism	Homo sapiens

Entity 2 branched

description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	3

Entity 3 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	6

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	42

Entity 5 non-polymer

description	BILIVERDINE IX ALPHA
formula_weight	582.6 kDa
src_method	syn
entity_count	3

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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	2.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.30 Å
resolution_method	—
num_particles	86709

fit	/app/data/saxs_computation/w7/9w76/9w76.fit
pddf	/app/data/pr_computation/w7/9w76/9w76.pr.out
profile	/app/data/saxs_computation/w7/9w76/9w76.dat

sarbecovirus Rc-o319 S-trimer in a locked-2 conformation

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