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9qnc

RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1 C-terminus

Method: ELECTRON MICROSCOPY D_max: 153.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qnc
deposition_date	2025-03-24
title	RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1 C-terminus
keywords	RAD51 recombinase, RAD51AP1, filament modulation, homologous recombination, nucleotide hydrolysis, DNA BINDING PROTEIN; DNA 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	45.30 Å
rg_electron	45.33 Å
i0	842038000.00
molecular_weight	230340.0 kDa
excluded_volume	284630 Å³
envelope_volume	390100 Å³
shell_volume	70512 Å³
envelope_diameter	162.3 Å
shell_rg	50.74 Å
envelope_rg	45.10 Å
shape_rg	45.34 Å
total_rg	45.50 Å
total_atoms	16096
n_residues	2043
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	153.6 Å
rg_real	45.38 Å
rg_real_error	1.34 Å
i0_real	8.4200e+08
i0_real_error	1.6830e+07
rg_reciprocal	45.30 Å
i0_reciprocal	842000000.0000
total_estimate	0.8678
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.9 Å
skewness	0.330
kurtosis	-0.550
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	392300000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.849

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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	37009.1 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,C,E,G,I,K
atom_count	16096

MAMQMQLEANADTSVEEESFGPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDAKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	RAD51-associated protein 1
formula_weight	4502.1 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	B,D,F,H,J,L

GPSVKSPNQSLRLGLSRLARVKPLHPNATSTAALEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	DNA
formula_weight	18267.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Z

AACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAAC

Entity 4 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	7

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

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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	2.980 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.98 Å
resolution_method	—
num_particles	97029

fit	/app/data/saxs_computation/qn/9qnc/9qnc.fit
pddf	/app/data/pr_computation/qn/9qnc/9qnc.pr.out
profile	/app/data/saxs_computation/qn/9qnc/9qnc.dat

RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1 C-terminus

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)