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9ui9

structure of a 12 base pair Rad51 D-loop complex

Method: ELECTRON MICROSCOPY D_max: 184.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ui9
deposition_date	2025-04-15
title	structure of a 12 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	51.19 Å
rg_electron	51.75 Å
i0	1908090000.00
molecular_weight	338920.0 kDa
excluded_volume	413580 Å³
envelope_volume	554750 Å³
shell_volume	89042 Å³
envelope_diameter	194.7 Å
shell_rg	55.77 Å
envelope_rg	51.06 Å
shape_rg	51.77 Å
total_rg	51.77 Å
total_atoms	23613
n_residues	2894
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	184.3 Å
rg_real	51.29 Å
rg_real_error	1.99 Å
i0_real	1.9080e+09
i0_real_error	4.1830e+07
rg_reciprocal	51.11 Å
i0_reciprocal	1908000000.0000
total_estimate	0.8543
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	53.5 Å
skewness	0.408
kurtosis	-0.254
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	465300000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.755; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.930

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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	9

Polymer

type	polypeptide(L)
strand_id	E,F,G,H,I,A,B,C,D
atom_count	23613

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	U

CGGTGTCGAGTCAGCCTATTCTTTTTTTTTATTCAATTAAGCAAGTAC

Entity 3 polymer

description	DNA (48-MER)
formula_weight	14856.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

GTACTTGCTTAATTGAATGCGTGGGCGACGTAGGCTGACTCGACACCG

Entity 4 polymer

description	DNA (35-MER)
formula_weight	10580.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	L

TTTTTTTTTTTTCGTCGCCCACGCTTTTTTTTTTT

Entity 5 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	9

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	9

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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	3.42 Å
resolution_method	—
num_particles	45865

fit	/app/data/saxs_computation/ui/9ui9/9ui9.fit
pddf	/app/data/pr_computation/ui/9ui9/9ui9.pr.out
profile	/app/data/saxs_computation/ui/9ui9/9ui9.dat

structure of a 12 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)