[21-7B-001] 21 bp tensegrity triangle that propagates via blunt-end stacking on two sides and via sticky-end cohesion on one side

entry_id	9y3b
deposition_date	2025-09-02
title	[21-7B-001] 21 bp tensegrity triangle that propagates via blunt-end stacking on two sides and via sticky-end cohesion on one side
keywords	dna, tensegrity triangle, stacking, blunt; DNA
method	X-RAY DIFFRACTION

rg_guinier	26.38 Å
rg_electron	25.99 Å
i0	66938500.00
molecular_weight	38611.0 kDa
excluded_volume	37335 ų
envelope_volume	62947 ų
shell_volume	21611 ų
envelope_diameter	85.4 Å
shell_rg	31.08 Å
envelope_rg	25.59 Å
shape_rg	25.94 Å
total_rg	26.45 Å
total_atoms	2562
n_residues	126
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	79.8 Å
rg_real	26.29 Å
rg_real_error	0.64 Å
i0_real	6.6940e+07
i0_real_error	1.0050e+06
rg_reciprocal	26.32 Å
i0_reciprocal	66940000.0000
total_estimate	0.9196
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.6 Å
skewness	0.119
kurtosis	-0.656
angular_range	— – 0.3000 Å−1
current_alpha	0.0000
highest_alpha	1524000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.987; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

Unit Cell

length_a	88.743 Å
length_b	104.798 Å
length_c	264.190 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

Symmetry

space_group	C 2 2 21
int_tables_number	20
crystal_system	orthorhombic

Refinement

resolution	6.130 Å
resolution_low	48.710 Å
r_factor	0.3012
r_work	0.2987
r_free	0.3571

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/y3/9y3b/pr_distribution.json
• pr_output /app/data/pr_computation/y3/9y3b/9y3b.pr.out
• pr_plot /app/data/visualization/pr_computation/y3/9y3b/9y3b_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/y3/9y3b/9y3b.dat
• saxs_fit /app/data/saxs_computation/y3/9y3b/9y3b.fit
• saxs_log /app/data/saxs_computation/y3/9y3b/9y3b.log
• saxs_plot /app/data/visualization/saxs_computation/y3/9y3b/9y3b_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/y3/9y3b/9y3b.fit
pddf	/app/data/pr_computation/y3/9y3b/9y3b.pr.out
profile	/app/data/saxs_computation/y3/9y3b/9y3b.dat