CryoEM structure of the octamer MraZ in complex with 1 box promoter from Mycoplasma genitalium

entry_id	9sx6
deposition_date	2025-10-08
title	CryoEM structure of the octamer MraZ in complex with 1 box promoter from Mycoplasma genitalium
keywords	MraZ, transcription factor, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	42.58 Å
rg_electron	40.88 Å
i0	353585000.00
molecular_weight	144730.0 kDa
excluded_volume	177030 ų
envelope_volume	249410 ų
shell_volume	49411 ų
envelope_diameter	132.9 Å
shell_rg	48.45 Å
envelope_rg	39.73 Å
shape_rg	40.76 Å
total_rg	41.64 Å
total_atoms	10133
n_residues	1154
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	134.6 Å
rg_real	42.49 Å
rg_real_error	0.98 Å
i0_real	3.5360e+08
i0_real_error	6.6520e+06
rg_reciprocal	42.58 Å
i0_reciprocal	353600000.0000
total_estimate	0.6756
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	58.2 Å
skewness	0.115
kurtosis	-0.731
angular_range	— – 0.1850 Å−1
current_alpha	0.0001
highest_alpha	24730000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 0.016; Positv: 1.000; Valcen: 0.995; Smooth: 0.851

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	3.570 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	3.57 Å
resolution_method	—
num_particles	49625

Files (7)

• pr_distribution /app/data/pr_computation/sx/9sx6/pr_distribution.json
• pr_output /app/data/pr_computation/sx/9sx6/9sx6.pr.out
• pr_plot /app/data/visualization/pr_computation/sx/9sx6/9sx6_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/sx/9sx6/9sx6.dat
• saxs_fit /app/data/saxs_computation/sx/9sx6/9sx6.fit
• saxs_log /app/data/saxs_computation/sx/9sx6/9sx6.log
• saxs_plot /app/data/visualization/saxs_computation/sx/9sx6/9sx6_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/sx/9sx6/9sx6.fit
pddf	/app/data/pr_computation/sx/9sx6/9sx6.pr.out
profile	/app/data/saxs_computation/sx/9sx6/9sx6.dat