SAXSdb — 11hr

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1. Structure Basics

entry_id	11hr
deposition_date	2026-02-25
title	Engineered IscB and wRNA bound to Target ssDNA
keywords	IscB, Cas9, HNH, CRISPR-Cas, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
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	36.12 Å
rg_electron	35.24 Å
i0	430242000.00
molecular_weight	119180.0 kDa
excluded_volume	128350 Å³
envelope_volume	187890 Å³
shell_volume	45174 Å³
envelope_diameter	124.3 Å
shell_rg	40.80 Å
envelope_rg	35.03 Å
shape_rg	35.18 Å
total_rg	35.63 Å
total_atoms	8088
n_residues	676
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	118.7 Å
rg_real	36.11 Å
rg_real_error	0.89 Å
i0_real	4.3020e+08
i0_real_error	7.2170e+06
rg_reciprocal	36.12 Å
i0_reciprocal	430200000.0000
total_estimate	0.8972
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.5 Å
skewness	0.276
kurtosis	-0.490
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0001
highest_alpha	21530000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.904

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	IscB
formula_weight	56779.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8088

MAVVYVISKSGKPLMPTTRCGHVRILLKEGKARVVERKPFTIQLTYESAEETQPLVLGIDPGRTNIGMSVVTESGESVFNAQLETRNKDVPKLMKDRKQYRRAHRRLKRRSKRRRRAKAAGTAFEEGEKQRLLPGCKKPITCKSIRNKEARFNNRKRPKGWLTPTANHLLVTHLNVVKKVQKILPVAKVVLELNRFSFMAMNNPKVQRWQYQRGPLYGKGSVEEAVSMQQDGHCLFCKHGIDHYHHVVPRRKNGSETLENRVGLCEEHHRLVHTDKEWEARLASKKSGMNKKYHALSVLNQIIPYLADQLADMFPGNFSVTSGRDTRLFREEHGIPKDHYLDAYCIACSALTDAKKVSSPKGRPYMVRQFRRHDRQASHKANLNRSYYMGGKKVATNRHKAMDQKTDSLEEYRAAHSAADVSKLTVKHPSAQYKDMSRIMPGSILVSGEGKLFTLSRSEGRNKGQVNYFVSTEGIKYWARKCQYLRNNGGLQIYV

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	RNA (233-MER)
formula_weight	75414.8 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

AAAAGAGUGAACGAGAGGCUCUUUCAACUUGAAAAGGUUGAAAGAGCACAGGCUGAGACAUUCGUAAGGCCGAAAGGCCGGACGCACCCUGGGAUUUCCCCAGUCCCCGGAACUGCAUAGCGGAUGUCAGUUGAUCGGCCGAGUAAUUUACGUCGACGUUGACGUCGAUGGUUGCGGCCGAUCAGAUAAGCCAGGGGGAACAAUCACCUCUCUGGAAACAGAGAGAGUUUUAC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 polymer

description	Target ssDNA
formula_weight	8405.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

TCTTCTAGTCTCGTTCACTCTTTTCTCT

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	293636

fit	/app/data/saxs_computation/1h/11hr/11hr.fit
pddf	/app/data/pr_computation/1h/11hr/11hr.pr.out
profile	/app/data/saxs_computation/1h/11hr/11hr.dat

Engineered IscB and wRNA bound to Target ssDNA

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)