Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub

entry_id	9q8y
deposition_date	2025-02-25
title	Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub
keywords	Ubiquitination, linchpin, RING ligase, LIGASE; LIGASE
method	X-RAY DIFFRACTION

rg_guinier	26.91 Å
rg_electron	25.99 Å
i0	57070000.00
molecular_weight	57781.0 kDa
excluded_volume	71851 ų
envelope_volume	95304 ų
shell_volume	30852 ų
envelope_diameter	91.3 Å
shell_rg	32.72 Å
envelope_rg	26.34 Å
shape_rg	26.01 Å
total_rg	26.68 Å
total_atoms	7814
n_residues	538
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	86.8 Å
rg_real	26.85 Å
rg_real_error	0.51 Å
i0_real	5.7070e+07
i0_real_error	7.5360e+05
rg_reciprocal	26.87 Å
i0_reciprocal	57070000.0000
total_estimate	0.8928
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.9 Å
skewness	0.296
kurtosis	-0.305
angular_range	— – 0.2950 Å−1
current_alpha	0.0000
highest_alpha	15520000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.943

Unit Cell

length_a	116.079 Å
length_b	116.079 Å
length_c	90.315 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

Symmetry

space_group	P 62
int_tables_number	171
crystal_system	hexagonal

Refinement

resolution	2.630 Å
resolution_low	43.920 Å
r_factor	0.2338
r_work	0.2317
r_free	0.2746

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/q8/9q8y/pr_distribution.json
• pr_output /app/data/pr_computation/q8/9q8y/9q8y.pr.out
• pr_plot /app/data/visualization/pr_computation/q8/9q8y/9q8y_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/q8/9q8y/9q8y.dat
• saxs_fit /app/data/saxs_computation/q8/9q8y/9q8y.fit
• saxs_log /app/data/saxs_computation/q8/9q8y/9q8y.log
• saxs_plot /app/data/visualization/saxs_computation/q8/9q8y/9q8y_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/q8/9q8y/9q8y.fit
pddf	/app/data/pr_computation/q8/9q8y/9q8y.pr.out
profile	/app/data/saxs_computation/q8/9q8y/9q8y.dat