SAXSdb — 9w04

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1. Structure Basics

entry_id	9w04
deposition_date	2025-07-23
title	Cryo-EM structure of TasH-tigRNA-dsDNA complex
keywords	protein complex, ANTIVIRAL PROTEIN; ANTIVIRAL 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	28.77 Å
rg_electron	28.33 Å
i0	242715000.00
molecular_weight	100520.0 kDa
excluded_volume	115760 Å³
envelope_volume	149770 Å³
shell_volume	42678 Å³
envelope_diameter	94.5 Å
shell_rg	36.96 Å
envelope_rg	28.25 Å
shape_rg	28.35 Å
total_rg	28.92 Å
total_atoms	6927
n_residues	710
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	88.5 Å
rg_real	28.67 Å
rg_real_error	0.43 Å
i0_real	2.4270e+08
i0_real_error	3.1340e+06
rg_reciprocal	28.71 Å
i0_reciprocal	242700000.0000
total_estimate	0.8961
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.4 Å
skewness	0.252
kurtosis	-0.360
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	46060000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.891

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	HNH nuclease domain-containing protein
formula_weight	40031.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6927

MNKQVLKEQASHCEITGAPLAGLPELVDVDRITERFQGGTYTPDNTRVLTPRAHMERHGILRERDQWLEELKAMMDDRAQTMKVVMKMNNQLLAYQRQTDHARQSTEQFLQDTLDASNKRLAQIDREVTKHIKHAKDPLAQAAMGVPGVGPITVAGLQTYVDLEKAKSASALWAYIGIDKPSHDRYTKGEAGGGNKTLRTMVWNMANSMIKNRKCPYRTVYEQTKERLAVSEKVTKSRNTQGQLIECAWKDTKPSHRHGAALRAVMKHFLADYWFVGRELAGLDTRPLYVQEKLGHTGIVQPQERGWEWGGSWSHPQFEKGGGSGGGSGGSAWSHPQFEKNLYFQSGSHHHHHH

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
host_organism	Escherichia coli

Entity 2 polymer

description	RNA (36-MER)
formula_weight	11948.2 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

AGUCAUUCCGUUAAAGACAACCACGGAGACGAAGCGA

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
host_organism	Escherichia coli

Entity 3 polymer

description	DNA (38-MER)
formula_weight	11606.5 kDa
src_method	man
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	D,E

CCCTAAGGCAATTCCGTTACGTCTCCGTGTTACAGGAC

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
host_organism	Escherichia coli

Entity 4 polymer

description	DNA (38-MER)
formula_weight	11784.6 kDa
src_method	man
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	F,G

GTCCTGTAACACGGAGACGTAACGGAATTGCCTTAGGG

Source

organism	Salicola phage CGphi29
ncbi_taxonomy_id	754067
host_organism	Escherichia coli

Entity 5 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	2.33 Å
resolution_method	—
num_particles	242496

fit	/app/data/saxs_computation/w0/9w04/9w04.fit
pddf	/app/data/pr_computation/w0/9w04/9w04.pr.out
profile	/app/data/saxs_computation/w0/9w04/9w04.dat

Cryo-EM structure of TasH-tigRNA-dsDNA 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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)