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9xvo

Crystal structure of NFIC monomer bound to DNA

Method: X-RAY DIFFRACTION D_max: 81.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xvo
deposition_date	2025-11-26
title	Crystal structure of NFIC 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	25.81 Å
rg_electron	25.32 Å
i0	57580100.00
molecular_weight	51160.0 kDa
excluded_volume	60791 Å³
envelope_volume	79326 Å³
shell_volume	26834 Å³
envelope_diameter	83.7 Å
shell_rg	31.92 Å
envelope_rg	24.91 Å
shape_rg	25.32 Å
total_rg	25.98 Å
total_atoms	3537
n_residues	369
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	81.3 Å
rg_real	25.80 Å
rg_real_error	0.53 Å
i0_real	5.7580e+07
i0_real_error	7.6830e+05
rg_reciprocal	25.81 Å
i0_reciprocal	57580000.0000
total_estimate	0.9046
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.317
kurtosis	-0.445
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	4182000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.941

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Nuclear factor 1 C-type
formula_weight	19393.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3597

GQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKDEERAVKDELLGEKPEVKQKWASRLLAKLRKDIRPECREDFVLSITGKKAPGCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKAAQCGHPVLCVQPHHIGVAVKE

Source

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

Entity 2 polymer

description	;DNA (5'-D(APAPGPTPTPGPGPCPAPCPCPGPTPGPCPCPAPAPCPTPT())-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(APAPGPTPTPGPGPCPAPCPGPGPTPGPCPCPAPAPCPTPT())-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 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	60

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6. Citations (1)

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length_a	61.917 Å
length_b	66.273 Å
length_c	140.433 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.500 Å
resolution_low	33.140 Å
r_factor	0.2059
r_work	0.2041
r_free	0.2387

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

Crystal structure of NFIC 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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)