SAXSdb — 9vx1

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1. Structure Basics

entry_id	9vx1
deposition_date	2025-07-18
title	The cryo-EM structure of gRNA-bound SPARDA complex
keywords	Cryo-EM, pAgo, DREN-APAZ, CELL INVASION; CELL INVASION
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	36.56 Å
rg_electron	35.78 Å
i0	426934000.00
molecular_weight	164200.0 kDa
excluded_volume	204210 Å³
envelope_volume	270830 Å³
shell_volume	61754 Å³
envelope_diameter	121.3 Å
shell_rg	43.42 Å
envelope_rg	34.75 Å
shape_rg	35.78 Å
total_rg	36.30 Å
total_atoms	11572
n_residues	1436
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	115.3 Å
rg_real	36.37 Å
rg_real_error	0.60 Å
i0_real	4.2690e+08
i0_real_error	6.9050e+06
rg_reciprocal	36.49 Å
i0_reciprocal	427000000.0000
total_estimate	0.8977
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.6 Å
skewness	0.154
kurtosis	-0.494
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0001
highest_alpha	79560000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.916

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	pAgo
formula_weight	54492.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	11572

MTFETRIFDEPELEFGDHHHHQDPRLGLSEAGPLQTFLGDVIKIGVVGNSKTIEDTRKFIETVSSGVEGKGEKHPNMHPPFPGLGNQSPYRCRFEIEDGATAALTKSKLDKIGKEPDHYRAVEMAVDEIIGELQAMDDGGSRPDVAIIALPVKLLERVWNAKVDARGTTEKSDSSGSDAPNFRGMLKAKAMGLSFPIQIVWEDVIDDKVTIPQKVKESSSRKIQDIAGRTWNLMTSLYYKGSGRIPWRRMPLEGEFSACYVGISFYREADGQQLFTSAAQMFDERGRGFVLKGRRARTESRGRHPYMAREDAKKIIEDVLAAYKLHHKTLPARVFILKTSRFKDEEADGIIAALDEAGTELRDLVWVQESYTARILRDGNYPVLRGTFVDLHGKGLLYTSGSMPYYGTYPGKYDPNPLLLCPHHTSESTVAQLAEEIFSLTKVNWNSTQMNQRLPIPIRAARKVGEVLKYVGEGEVISADYRKYI

Source

organism	Novosphingopyxis baekryungensis
ncbi_taxonomy_id	279369
host_organism	Bacteria Latreille et al. 1825

Entity 2 polymer

description	DREN-APAZ
formula_weight	50419.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MTKKITANQIIGEIGENEVRGRFLTLGWQFDGRSRLEAGIDGIAEVMNEGQPMARMIAVQIKSTKEGKYTSESDTSFTYLLRTQDLAYWRGSNLPVIVVFYRQSDHSFYWKEVSRDAGPGERRLNIDKVADLFNASTVNKLAALTVPKTGLGYYVPPLGGGEDALINMLPLTLPNEMYIASTTYEPRKAIAVILNGDGPKRFDWVINGGTFWSFHDPRTSACSEIVDIDQVEAINTKELALHDDIDEQNRFSHLLRQTLRYQTDSDLGWDKDHKALYFRAIEREVSRNFAYTSSKKKTDANVVSVFKNSKDETRVSFVRHHAFSPRFELMADQWYLIITPTYYYTTNGYAPHQFAAPLLAGKKRLDKSAALRGQVIMWHRFLTQSDHEDLFHSEETPEAYLMFGEPPSIHLDVRVPEDGWVKEKVKRIDEAAQGEGLFSDDI

Source

organism	Novosphingopyxis baekryungensis
ncbi_taxonomy_id	279369
host_organism	Bacteria Latreille et al. 1825

Entity 3 polymer

description	;RNA (5'-R(PAPUPAPCPUPGPCPAPCPAPGPCPUPGPAPCPGPAPUPA)-3') ;
formula_weight	6390.9 kDa
src_method	man
entity_count	2

Polymer

type	polyribonucleotide
strand_id	Z,a

AUACUGCACAGCUGACGAUA

Source

organism	Novosphingopyxis baekryungensis
ncbi_taxonomy_id	279369
host_organism	Novosphingopyxis baekryungensis

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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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	2.77 Å
resolution_method	—
num_particles	98314

fit	/app/data/saxs_computation/vx/9vx1/9vx1.fit
pddf	/app/data/pr_computation/vx/9vx1/9vx1.pr.out
profile	/app/data/saxs_computation/vx/9vx1/9vx1.dat

The cryo-EM structure of gRNA-bound SPARDA complex

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)