SAXSdb — 9vx6

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1. Structure Basics

entry_id	9vx6
deposition_date	2025-07-18
title	Helical structure of gRNA-tDNA SPARDA complex
keywords	Cryo-EM, SPARDA, pAgo, 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	53.93 Å
rg_electron	53.05 Å
i0	3395120000.00
molecular_weight	448440.0 kDa
excluded_volume	544200 Å³
envelope_volume	766670 Å³
shell_volume	117330 Å³
envelope_diameter	178.2 Å
shell_rg	57.95 Å
envelope_rg	52.60 Å
shape_rg	53.02 Å
total_rg	53.26 Å
total_atoms	31391
n_residues	3634
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	176.6 Å
rg_real	53.73 Å
rg_real_error	1.29 Å
i0_real	3.3950e+09
i0_real_error	6.5940e+07
rg_reciprocal	54.09 Å
i0_reciprocal	3397000000.0000
total_estimate	0.8799
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	73.1 Å
skewness	0.148
kurtosis	-0.456
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	440100000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.857

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	target DNA
formula_weight	6140.0 kDa
src_method	man
entity_count	4

Polymer

type	polydeoxyribonucleotide
strand_id	L,E,I,Q
atom_count	31391

TATCGTCAGCTGTGCAGTAT

Source

organism	Bacteriophage sp.
ncbi_taxonomy_id	38018
host_organism	Bacteriophage sp.

Entity 2 polymer

description	guide RNA
formula_weight	6390.9 kDa
src_method	man
entity_count	4

Polymer

type	polyribonucleotide
strand_id	R,F,J,V

AUACUGCACAGCUGACGAUA

Source

organism	Novosphingopyxis baekryungensis
ncbi_taxonomy_id	279369
host_organism	Novosphingopyxis baekryungensis

Entity 3 polymer

description	pAGO
formula_weight	54492.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	S,O,W,U

MTFETRIFDEPELEFGDHHHHQDPRLGLSEAGPLQTFLGDVIKIGVVGNSKTIEDTRKFIETVSSGVEGKGEKHPNMHPPFPGLGNQSPYRCRFEIEDGATAALTKSKLDKIGKEPDHYRAVEMAVDEIIGELQAMDDGGSRPDVAIIALPVKLLERVWNAKVDARGTTEKSDSSGSDAPNFRGMLKAKAMGLSFPIQIVWEDVIDDKVTIPQKVKESSSRKIQDIAGRTWNLMTSLYYKGSGRIPWRRMPLEGEFSACYVGISFYREADGQQLFTSAAQMFDERGRGFVLKGRRARTESRGRHPYMAREDAKKIIEDVLAAYKLHHKTLPARVFILKTSRFKDEEADGIIAALDEAGTELRDLVWVQESYTARILRDGNYPVLRGTFVDLHGKGLLYTSGSMPYYGTYPGKYDPNPLLLCPHHTSESTVAQLAEEIFSLTKVNWNSTQMNQRLPIPIRAARKVGEVLKYVGEGEVISADYRKYI

Source

organism	Novosphingopyxis baekryungensis
ncbi_taxonomy_id	279369
host_organism	Novosphingopyxis baekryungensis

Entity 4 polymer

description	DREN-APAZ
formula_weight	50419.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	T,P,Y,X

MTKKITANQIIGEIGENEVRGRFLTLGWQFDGRSRLEAGIDGIAEVMNEGQPMARMIAVQIKSTKEGKYTSESDTSFTYLLRTQDLAYWRGSNLPVIVVFYRQSDHSFYWKEVSRDAGPGERRLNIDKVADLFNASTVNKLAALTVPKTGLGYYVPPLGGGEDALINMLPLTLPNEMYIASTTYEPRKAIAVILNGDGPKRFDWVINGGTFWSFHDPRTSACSEIVDIDQVEAINTKELALHDDIDEQNRFSHLLRQTLRYQTDSDLGWDKDHKALYFRAIEREVSRNFAYTSSKKKTDANVVSVFKNSKDETRVSFVRHHAFSPRFELMADQWYLIITPTYYYTTNGYAPHQFAAPLLAGKKRLDKSAALRGQVIMWHRFLTQSDHEDLFHSEETPEAYLMFGEPPSIHLDVRVPEDGWVKEKVKRIDEAAQGEGLFSDDI

Source

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

Entity 5 polymer

description	substrate ssDNA
formula_weight	3364.2 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	M

CTGTGCAGTAT

Source

organism	Bacteriophage sp.
ncbi_taxonomy_id	38018
host_organism	Bacteriophage sp.

Entity 6 polymer

description	substrate ssRNA
formula_weight	3466.1 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	N

UACUGCACAGC

Source

organism	Novosphingopyxis baekryungensis
ncbi_taxonomy_id	279369
host_organism	Novosphingopyxis baekryungensis

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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	2.64 Å
resolution_method	—
num_particles	57938

fit	/app/data/saxs_computation/vx/9vx6/9vx6.fit
pddf	/app/data/pr_computation/vx/9vx6/9vx6.pr.out
profile	/app/data/saxs_computation/vx/9vx6/9vx6.dat

Helical structure of gRNA-tDNA 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 (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 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)