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9xvq

Crystal structure of the NFIA-N0 DNA complex

Method: X-RAY DIFFRACTION D_max: 65.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xvq
deposition_date	2025-11-26
title	Crystal structure of the NFIA-N0 DNA complex
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	19.90 Å
rg_electron	18.51 Å
i0	13365300.00
molecular_weight	24166.0 kDa
excluded_volume	28968 Å³
envelope_volume	37277 Å³
shell_volume	17448 Å³
envelope_diameter	67.6 Å
shell_rg	24.17 Å
envelope_rg	18.80 Å
shape_rg	18.47 Å
total_rg	19.44 Å
total_atoms	1675
n_residues	178
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	65.1 Å
rg_real	19.80 Å
rg_real_error	0.47 Å
i0_real	1.3370e+07
i0_real_error	1.9750e+05
rg_reciprocal	19.82 Å
i0_reciprocal	13370000.0000
total_estimate	0.8052
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.7 Å
skewness	0.198
kurtosis	-0.254
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	930600.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Nuclear factor 1 A-type
formula_weight	26321.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1927

GDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSVTELVRVSQTPIAA

Source

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

Entity 2 polymer

description	;DNA (5'-D(APAPGPTPTPGPGPCPAPTPGPCPCPAPAPCPTPT)-3') ;
formula_weight	5211.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

AAGTTGGCATGCCAACT

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	252

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6. Citations (1)

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length_a	48.501 Å
length_b	113.243 Å
length_c	128.117 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 21 21 21
int_tables_number	24
crystal_system	—

resolution	1.760 Å
resolution_low	36.210 Å
r_factor	0.1962
r_work	0.1948
r_free	0.2220

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

Crystal structure of the NFIA-N0 DNA 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

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)