Crystal structure for YxiD-YxxD toxin-immunity protein complex from Bacillus subtilis 6633.

entry_id	9v8i
deposition_date	2025-05-29
last_revision	2025-12-24
title	Crystal structure for YxiD-YxxD toxin-immunity protein complex from Bacillus subtilis 6633.
keywords	Toxin, YxiD, YxxD, Immunity-protein, tRNase, Bacillus subtilis 6633; TOXIN
method	X-RAY DIFFRACTION

rg_guinier	18.51 Å
rg_electron	17.45 Å
i0	10766500.00
molecular_weight	24380.0 kDa
excluded_volume	30492 ų
envelope_volume	35667 ų
shell_volume	17156 ų
envelope_diameter	59.1 Å
shell_rg	23.55 Å
envelope_rg	17.73 Å
shape_rg	17.41 Å
total_rg	18.52 Å
total_atoms	1727
n_residues	215
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	58.8 Å
rg_real	18.42 Å
rg_real_error	0.35 Å
i0_real	1.0770e+07
i0_real_error	1.2960e+05
rg_reciprocal	18.43 Å
i0_reciprocal	10770000.0000
total_estimate	0.8168
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	22.6 Å
skewness	0.195
kurtosis	-0.405
angular_range	— – 0.4300 Å−1
current_alpha	0.0000
highest_alpha	2538000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

Unit Cell

length_a	67.378 Å
length_b	70.890 Å
length_c	91.788 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	—

Refinement

resolution	1.700 Å
resolution_low	33.440 Å
r_factor	0.1878
r_work	0.1859
r_free	0.2271

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/v8/9v8i/pr_distribution.json
• pr_output /app/data/pr_computation/v8/9v8i/9v8i.pr.out
• pr_plot /app/data/visualization/pr_computation/v8/9v8i/9v8i_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/v8/9v8i/9v8i.dat
• saxs_fit /app/data/saxs_computation/v8/9v8i/9v8i.fit
• saxs_log /app/data/saxs_computation/v8/9v8i/9v8i.log
• saxs_plot /app/data/visualization/saxs_computation/v8/9v8i/9v8i_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/v8/9v8i/9v8i.fit
pddf	/app/data/pr_computation/v8/9v8i/9v8i.pr.out
profile	/app/data/saxs_computation/v8/9v8i/9v8i.dat