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9xvf

Crystal structure of NFIA monomer bound to DNA

Method: X-RAY DIFFRACTION D_max: 80.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xvf
deposition_date	2025-11-26
last_revision	2026-01-21
title	Crystal structure of NFIA monomer bound to DNA
keywords	Transcription factor, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	25.74 Å
rg_electron	25.45 Å
i0	55811100.00
molecular_weight	50238.0 kDa
excluded_volume	59614 Å³
envelope_volume	77951 Å³
shell_volume	26112 Å³
envelope_diameter	83.2 Å
shell_rg	32.15 Å
envelope_rg	25.08 Å
shape_rg	25.45 Å
total_rg	26.12 Å
total_atoms	3472
n_residues	360
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	80.4 Å
rg_real	25.74 Å
rg_real_error	0.51 Å
i0_real	5.5810e+07
i0_real_error	7.1330e+05
rg_reciprocal	25.74 Å
i0_reciprocal	55810000.0000
total_estimate	0.9082
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.315
kurtosis	-0.482
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	3948000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.965

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Nuclear factor 1 A-type
formula_weight	19463.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3575

GDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKE

Source

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

Entity 2 polymer

description	;DNA (5'-D(APAPGPTPTPGPGPCPAPCPCPGPTPGPCPCPAPAPCPTP*T)-3') ;
formula_weight	6423.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

AAGTTGGCACCGTGCCAACTT

Entity 3 polymer

description	;DNA (5'-D(APAPGPTPTPGPGPCPAPCPGPGPTPGPCPCPAPAPCPTP*T)-3') ;
formula_weight	6463.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

AAGTTGGCACGGTGCCAACTT

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	103

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6. Citations (1)

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length_a	83.677 Å
length_b	48.463 Å
length_c	105.882 Å
angle_alpha	90.00 °
angle_beta	92.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 2 1
int_tables_number	3
crystal_system	—

resolution	2.600 Å
resolution_low	19.970 Å
r_factor	0.1959
r_work	0.1931
r_free	0.2476

fit	/app/data/saxs_computation/xv/9xvf/9xvf.fit
pddf	/app/data/pr_computation/xv/9xvf/9xvf.pr.out
profile	/app/data/saxs_computation/xv/9xvf/9xvf.dat

Crystal structure of NFIA monomer bound to DNA

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)