Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to Trim16 IR1 Response Element

entry_id	9qj9
deposition_date	2025-03-18
last_revision	2026-01-28
title	Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to Trim16 IR1 Response Element
keywords	DNA complex, TRANSCRIPTION; TRANSCRIPTION
method	X-RAY DIFFRACTION

rg_guinier	18.55 Å
rg_electron	18.30 Å
i0	18609900.00
molecular_weight	25032.0 kDa
excluded_volume	27942 ų
envelope_volume	35627 ų
shell_volume	16620 ų
envelope_diameter	59.1 Å
shell_rg	23.81 Å
envelope_rg	18.23 Å
shape_rg	18.29 Å
total_rg	18.94 Å
total_atoms	1688
n_residues	168
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	58.4 Å
rg_real	18.47 Å
rg_real_error	0.33 Å
i0_real	1.8610e+07
i0_real_error	2.2140e+05
rg_reciprocal	18.49 Å
i0_reciprocal	18610000.0000
total_estimate	0.8308
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.8 Å
skewness	0.192
kurtosis	-0.514
angular_range	— – 0.4300 Å−1
current_alpha	0.0000
highest_alpha	2241000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

Unit Cell

length_a	56.019 Å
length_b	56.019 Å
length_c	169.871 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

Symmetry

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

Refinement

resolution	3.500 Å
resolution_low	33.842 Å
r_factor	0.2702
r_work	0.2668
r_free	0.3352

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/qj/9qj9/pr_distribution.json
• pr_output /app/data/pr_computation/qj/9qj9/9qj9.pr.out
• pr_plot /app/data/visualization/pr_computation/qj/9qj9/9qj9_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/qj/9qj9/9qj9.dat
• saxs_fit /app/data/saxs_computation/qj/9qj9/9qj9.fit
• saxs_log /app/data/saxs_computation/qj/9qj9/9qj9.log
• saxs_plot /app/data/visualization/saxs_computation/qj/9qj9/9qj9_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/qj/9qj9/9qj9.fit
pddf	/app/data/pr_computation/qj/9qj9/9qj9.pr.out
profile	/app/data/saxs_computation/qj/9qj9/9qj9.dat