Hna Dimer

Method: ELECTRON MICROSCOPY D_max: 140.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ykj
deposition_date	2025-10-07
title	Hna Dimer
keywords	PD(D/E)XK nuclease, Superfamily 2 helicase, Anti-bacteriophage protein, IMMUNE SYSTEM; IMMUNE SYSTEM
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	39.86 Å
rg_electron	40.57 Å
i0	159536000.00
molecular_weight	83369.0 kDa
excluded_volume	96186 Å³
envelope_volume	188340 Å³
shell_volume	42141 Å³
envelope_diameter	148.0 Å
shell_rg	41.75 Å
envelope_rg	40.03 Å
shape_rg	40.55 Å
total_rg	40.70 Å
total_atoms	5952
n_residues	1205
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	140.5 Å
rg_real	40.49 Å
rg_real_error	1.50 Å
i0_real	1.5950e+08
i0_real_error	3.0060e+06
rg_reciprocal	40.11 Å
i0_reciprocal	159500000.0000
total_estimate	0.7759
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.1 Å
skewness	0.620
kurtosis	-0.235
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	35130000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.605; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.676; Smooth: 0.591

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4. Crystallography & Experiment

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5. Entities & Polymer Info (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	4.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.40 Å
resolution_method	—
num_particles	183538

description	Helicase ATP-binding domain-containing protein
formula_weight	94841.2 kDa
src_method	man
entity_count	2

Hna Dimer

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Sinorhizobium meliloti
ncbi_taxonomy_id	382
host_organism	Escherichia coli

fit	/app/data/saxs_computation/yk/9ykj/9ykj.fit
pddf	/app/data/pr_computation/yk/9ykj/9ykj.pr.out
profile	/app/data/saxs_computation/yk/9ykj/9ykj.dat

type	polypeptide(L)
strand_id	A,B
atom_count	5952