Crystal structure of NFIC homodimer bound to DNA

entry_id	9xvd
deposition_date	2025-11-26
title	Crystal structure of NFIC homodimer bound to DNA
keywords	Transcription factor, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
method	X-RAY DIFFRACTION

rg_guinier	33.14 Å
rg_electron	32.96 Å
i0	229466000.00
molecular_weight	106450.0 kDa
excluded_volume	126990 ų
envelope_volume	172790 ų
shell_volume	44116 ų
envelope_diameter	115.5 Å
shell_rg	39.46 Å
envelope_rg	32.44 Å
shape_rg	32.98 Å
total_rg	33.35 Å
total_atoms	7370
n_residues	773
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	108.7 Å
rg_real	33.10 Å
rg_real_error	0.83 Å
i0_real	2.2950e+08
i0_real_error	3.6030e+06
rg_reciprocal	33.12 Å
i0_reciprocal	229500000.0000
total_estimate	0.8896
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.5 Å
skewness	0.312
kurtosis	-0.331
angular_range	— – 0.2400 Å−1
current_alpha	0.0000
highest_alpha	22940000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.893

Unit Cell

length_a	83.457 Å
length_b	84.290 Å
length_c	146.710 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

Symmetry

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

Refinement

resolution	2.600 Å
resolution_low	18.270 Å
r_factor	0.1945
r_work	0.1912
r_free	0.2536

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/xv/9xvd/pr_distribution.json
• pr_output /app/data/pr_computation/xv/9xvd/9xvd.pr.out
• pr_plot /app/data/visualization/pr_computation/xv/9xvd/9xvd_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/xv/9xvd/9xvd.dat
• saxs_fit /app/data/saxs_computation/xv/9xvd/9xvd.fit
• saxs_log /app/data/saxs_computation/xv/9xvd/9xvd.log
• saxs_plot /app/data/visualization/saxs_computation/xv/9xvd/9xvd_saxs_profile.png

Curves (3)

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