Structure of NONO bound to (R)-SKBG-1 in P43212

Method: X-RAY DIFFRACTION D_max: 74.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qzl
deposition_date	2025-04-23
last_revision	2025-12-17
title	Structure of NONO bound to (R)-SKBG-1 in P43212
keywords	DBHS, Paraspeckle, Ligand, RNA BINDING PROTEIN; RNA BINDING PROTEIN
method	X-RAY DIFFRACTION

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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	25.69 Å
rg_electron	24.96 Å
i0	103221000.00
molecular_weight	52621.0 kDa
excluded_volume	50604 Å³
envelope_volume	91821 Å³
shell_volume	30672 Å³
envelope_diameter	76.4 Å
shell_rg	32.30 Å
envelope_rg	24.65 Å
shape_rg	24.95 Å
total_rg	25.60 Å
total_atoms	3987
n_residues	483
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	74.5 Å
rg_real	25.53 Å
rg_real_error	0.37 Å
i0_real	1.0320e+08
i0_real_error	1.1400e+06
rg_reciprocal	25.58 Å
i0_reciprocal	103200000.0000
total_estimate	0.9172
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.4 Å
skewness	0.073
kurtosis	-0.620
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	8920000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.987; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	87.069 Å
length_b	87.069 Å
length_c	138.587 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	2.900 Å
resolution_low	19.870 Å
r_factor	0.2068
r_work	0.2034
r_free	0.2712

description	Non-POU domain-containing octamer-binding protein
formula_weight	30147.5 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	3995

Structure of NONO bound to (R)-SKBG-1 in P43212

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

Diffraction

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

description	4-(2-chloranylethanoyl)-~{N}-[(4-methoxyphenyl)methyl]-1-(4-methoxyphenyl)sulfonyl-piperazine-2-carboxamide
formula_weight	496.0 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/qz/9qzl/9qzl.fit
pddf	/app/data/pr_computation/qz/9qzl/9qzl.pr.out
profile	/app/data/saxs_computation/qz/9qzl/9qzl.dat