SAXSdb — 9sjd

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1. Structure Basics

entry_id	9sjd
deposition_date	2025-08-31
title	Type I-F_HNH variant Cascade bound to dsDNA, HNH domain in outwards position
keywords	CRISPR-Cas Type I-F HNH nuclease, RNA BINDING PROTEIN; RNA BINDING 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	50.01 Å
rg_electron	49.72 Å
i0	1709090000.00
molecular_weight	331040.0 kDa
excluded_volume	407520 Å³
envelope_volume	557250 Å³
shell_volume	89353 Å³
envelope_diameter	159.7 Å
shell_rg	58.41 Å
envelope_rg	47.94 Å
shape_rg	49.73 Å
total_rg	49.92 Å
total_atoms	23176
n_residues	2713
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	159.6 Å
rg_real	49.83 Å
rg_real_error	1.33 Å
i0_real	1.7090e+09
i0_real_error	3.2960e+07
rg_reciprocal	50.14 Å
i0_reciprocal	1710000000.0000
total_estimate	0.8931
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	77.2 Å
skewness	0.017
kurtosis	-0.737
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	265200000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Cas8f
formula_weight	39339.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	23176

MLRNKILAAISQKIPEEQKINKYIEGLFQSIDKNHLATHVAKFTETNSPGNIGAYDILSSDMNCGYLDTANAGWKEPDIVTNDAKYKRPQGFVAMEMSDGRTVMEHLQEDSAELRHEMEELTDKYDEIRDGILNMPSMQPYRTNQFIKQVFFPVGGSYHLLSILPSTVLNYEVSDRLYRSKIPKIRLRLLSSNAASTTGSRLVSKNKWPLVFQALPPKFLEKNLAKALDKEYLLPDINIDELEGVDNGCLIDEALLPLIIDEGKRKGEGNYRPRHLRDERKEETVQAFLDKYGYCNIPVGYEVHHIVPLSQGGADSIKNMIMLSIEHHERVTEAHASYFKWRNT

Source

organism	Selenomonas sp.
ncbi_taxonomy_id	2053611
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Cas5f
formula_weight	28703.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MMKGYILLEKVNIENANAFNNIIVGIPAITSFLGFARALERKLNAKEIAIRINGVGLEFHEYELKGYKNKRGQYVTSCPLPGSIPGQNEKKLDAHIMNQAYIDLNMSFLLEVEGPHVDMSTCKSIKSTMETLRIAGGIIRNYKKIRLIDTLADIPYGYFLTLRQDNLNDAAGDDMLDKMIHALQQEDTLVPIAVGFKALSEVGHVEGQRDPEKDHCFVESIFSLGGFECSKILEDINSCLWRYKTEEGLYLCTII

Source

organism	Selenomonas sp.
ncbi_taxonomy_id	2053611
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Cas6f
formula_weight	20735.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MFSQILIIKPGTGISPNIIISEDIFPVLHSLFVEHDKKFGITFPAYSFDKKGHLGNIIEVLSEDKEALASLCLEEHLAEVTDYVKVKKEITFTDDYVLFKRIREENQYETTARRMRKRGHTELGRPLEMHIKKKNQQIFCHAYIKVKSASTGQSYNIFLAPTDIKHGSFSAYGLLRGDTHA

Source

organism	Selenomonas sp.
ncbi_taxonomy_id	2053611
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Non-target strand
formula_weight	14233.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	L

AAAAAGCGGAGAAGTCATTTAATAAGGCCACTGTTAAAAACCGTAC

Entity 5 polymer

description	Cas7f
formula_weight	38700.2 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	D,E,F,C,G,H

MAANKKATNVTLKSRPENLSFARCLNTTEAKFWQTDFLKRHTFKLPLLITDKAVLASKGHEMPPDKLEKEIMDPNPQKSQSCTLSTECDTLRIDFGIKVLPVKESMYSCSDYNYRTAIYQKIDEYIAEDGFLTLAKRYVNNIANARFLWRNRKGAEIIETIVTIEDKEYPSFNSKSFNLDTFVEDNATINEIAQQIADTFAGKREYLNIYVTCFVKIGCAMEVYPSQEMTFDDDDKGKKLFKFEGSAGMHSQKINNALRTIDTWYPDYTTYEFPIPVENYGAARSIGIPFRPDTKSFYKLIDRMILKNEDLPIEDKHYVMAILIRGGMFSKKQEK

Source

organism	Selenomonas sp.
ncbi_taxonomy_id	2053611
host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

description	Target strand
formula_weight	14094.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	K

GTACGGTTTTTAACAGTGGCCTTATTAAATGACTTCTCCGCTTTTT

Entity 7 polymer

description	crRNA
formula_weight	19440.6 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	J

UUUAGAAGGAGAAGUCAUUUAAUAAGGCCACUGUUAAAAAGUGUACCGCCGGAUAGGCGG

Source

organism	Selenomonas sp.
ncbi_taxonomy_id	2053611
host_organism	Escherichia coli BL21(DE3)

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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	triclinic

resolution	3.05 Å
resolution_method	—
num_particles	24776

fit	/app/data/saxs_computation/sj/9sjd/9sjd.fit
pddf	/app/data/pr_computation/sj/9sjd/9sjd.pr.out
profile	/app/data/saxs_computation/sj/9sjd/9sjd.dat

Type I-F_HNH variant Cascade bound to dsDNA, HNH domain in outwards position

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)