SAXSdb — 9ui7

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1. Structure Basics

entry_id	9ui7
deposition_date	2025-04-15
title	structure of a 4 base pair Rad51 D-loop complex
keywords	homologous recombination, strand exchange, D-loop, RECOMBINATION, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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	45.85 Å
rg_electron	46.10 Å
i0	1230270000.00
molecular_weight	267740.0 kDa
excluded_volume	325770 Å³
envelope_volume	448780 Å³
shell_volume	79955 Å³
envelope_diameter	164.9 Å
shell_rg	51.25 Å
envelope_rg	45.73 Å
shape_rg	46.12 Å
total_rg	46.23 Å
total_atoms	18640
n_residues	2267
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	155.2 Å
rg_real	45.86 Å
rg_real_error	1.60 Å
i0_real	1.2300e+09
i0_real_error	2.5750e+07
rg_reciprocal	45.85 Å
i0_reciprocal	1230000000.0000
total_estimate	0.8783
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.2 Å
skewness	0.340
kurtosis	-0.384
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	263800000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.858

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DNA repair protein RAD51 homolog 1
formula_weight	39557.8 kDa
mutation	S208E/A209D
src_method	man
entity_count	7

Polymer

type	polypeptide(L)
strand_id	D,E,F,G,A,C,B
atom_count	18645

MASWSHPQFEKGADDDDKVPDPMAMQMQLEASADTSVEEESFGPQPISRLEQCGINANDVKKLEEAGYHTVEAVAYAPKKELINIKGISEAKADKILTEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARGFNTDHQTQLLYQAEDMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDAKD

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (48-MER)
formula_weight	14720.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	H

CGGTGTCGAGTCAGCCTATTCTTTTTTTTTATTCAATTAAGCAAGTAC

Entity 3 polymer

description	DNA (48-MER)
formula_weight	14857.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

GTACTTGCTTAATTGAATAAAAGGGCGACGTAGGCTGACTCGACACCG

Entity 4 polymer

description	DNA (27-MER)
formula_weight	8147.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	L

TTTCGTCGCCCACGCTTTTTTTTTTTT

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	7

Entity 6 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	7

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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	3.91 Å
resolution_method	—
num_particles	14688

fit	/app/data/saxs_computation/ui/9ui7/9ui7.fit
pddf	/app/data/pr_computation/ui/9ui7/9ui7.pr.out
profile	/app/data/saxs_computation/ui/9ui7/9ui7.dat

structure of a 4 base pair Rad51 D-loop 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

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)