Cryo-EM structure of Z22 antibody in complex with left-handed Z-DNA (trimer)

entry_id	9tgw
deposition_date	2025-12-02
title	Cryo-EM structure of Z22 antibody in complex with left-handed Z-DNA (trimer)
keywords	Z-DNA, left-handed geometry, monoclonal antibody, antibody avidity, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	29.80 Å
rg_electron	29.94 Å
i0	127712000.00
molecular_weight	83157.0 kDa
excluded_volume	101220 ų
envelope_volume	131130 ų
shell_volume	36630 ų
envelope_diameter	106.2 Å
shell_rg	36.96 Å
envelope_rg	29.85 Å
shape_rg	29.91 Å
total_rg	30.62 Å
total_atoms	5814
n_residues	705
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	102.3 Å
rg_real	29.72 Å
rg_real_error	0.91 Å
i0_real	1.2770e+08
i0_real_error	1.8690e+06
rg_reciprocal	29.76 Å
i0_reciprocal	127700000.0000
total_estimate	0.8815
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.8 Å
skewness	0.249
kurtosis	-0.476
angular_range	— – 0.2650 Å−1
current_alpha	0.0000
highest_alpha	21380000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.997

Unit Cell

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

Symmetry

space_group	P 1
int_tables_number	1
crystal_system	—

Refinement

resolution	2.670 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	2.67 Å
resolution_method	—
num_particles	59879

Files (7)

• pr_distribution /app/data/pr_computation/tg/9tgw/pr_distribution.json
• pr_output /app/data/pr_computation/tg/9tgw/9tgw.pr.out
• pr_plot /app/data/visualization/pr_computation/tg/9tgw/9tgw_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/tg/9tgw/9tgw.dat
• saxs_fit /app/data/saxs_computation/tg/9tgw/9tgw.fit
• saxs_log /app/data/saxs_computation/tg/9tgw/9tgw.log
• saxs_plot /app/data/visualization/saxs_computation/tg/9tgw/9tgw_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/tg/9tgw/9tgw.fit
pddf	/app/data/pr_computation/tg/9tgw/9tgw.pr.out
profile	/app/data/saxs_computation/tg/9tgw/9tgw.dat