NF-YB/C Heterodimer in Complex with NF-YA-derived Stitched Peptide

entry_id	9r4d
deposition_date	2025-05-07
last_revision	2026-05-20
title	NF-YB/C Heterodimer in Complex with NF-YA-derived Stitched Peptide
keywords	transcription factor, crosslink, stitched peptide, NF-Y, TRANSCRIPTION; TRANSCRIPTION
method	X-RAY DIFFRACTION

rg_guinier	17.97 Å
rg_electron	16.91 Å
i0	18747800.00
molecular_weight	21958.0 kDa
excluded_volume	21260 ų
envelope_volume	34586 ų
shell_volume	17010 ų
envelope_diameter	63.2 Å
shell_rg	23.12 Å
envelope_rg	17.34 Å
shape_rg	16.89 Å
total_rg	17.72 Å
total_atoms	1667
n_residues	199
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	60.7 Å
rg_real	17.88 Å
rg_real_error	0.50 Å
i0_real	1.8750e+07
i0_real_error	2.6450e+05
rg_reciprocal	17.89 Å
i0_reciprocal	18750000.0000
total_estimate	0.6400
solution_quality	REASONABLE a REASONABLE solution
n_peaks	4
r_peak_primary	24.6 Å
skewness	0.227
kurtosis	-0.311
angular_range	— – 0.4450 Å−1
current_alpha	0.0000
highest_alpha	4895000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.648; Stabil: 0.937; Sysdev: 0.227; Positv: 1.000; Valcen: 1.000; Smooth: 0.880

Unit Cell

length_a	49.600 Å
length_b	53.500 Å
length_c	77.600 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

Symmetry

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

Refinement

resolution	1.700 Å
resolution_low	44.050 Å
r_factor	0.1702
r_work	0.1683
r_free	0.2062

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/r4/9r4d/pr_distribution.json
• pr_output /app/data/pr_computation/r4/9r4d/9r4d.pr.out
• pr_plot /app/data/visualization/pr_computation/r4/9r4d/9r4d_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/r4/9r4d/9r4d.dat
• saxs_fit /app/data/saxs_computation/r4/9r4d/9r4d.fit
• saxs_log /app/data/saxs_computation/r4/9r4d/9r4d.log
• saxs_plot /app/data/visualization/saxs_computation/r4/9r4d/9r4d_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/r4/9r4d/9r4d.fit
pddf	/app/data/pr_computation/r4/9r4d/9r4d.pr.out
profile	/app/data/saxs_computation/r4/9r4d/9r4d.dat