Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant

entry_id	9yea
deposition_date	2025-09-23
title	Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant
keywords	Ubiquitin conjugating enzyme, ubiquitin, conjugate, isopeptide, LIGASE; LIGASE
method	X-RAY DIFFRACTION

rg_guinier	21.43 Å
rg_electron	20.68 Å
i0	10455700.00
molecular_weight	24458.0 kDa
excluded_volume	30772 ų
envelope_volume	36293 ų
shell_volume	15897 ų
envelope_diameter	70.2 Å
shell_rg	25.40 Å
envelope_rg	20.73 Å
shape_rg	20.67 Å
total_rg	21.42 Å
total_atoms	1725
n_residues	224
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	71.8 Å
rg_real	21.54 Å
rg_real_error	0.51 Å
i0_real	1.0460e+07
i0_real_error	1.4200e+05
rg_reciprocal	21.52 Å
i0_reciprocal	10460000.0000
total_estimate	0.6700
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	19.0 Å
skewness	0.425
kurtosis	-0.418
angular_range	— – 0.3700 Å−1
current_alpha	0.0000
highest_alpha	3210000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 0.161; Positv: 1.000; Valcen: 0.833; Smooth: 0.985

Unit Cell

length_a	39.445 Å
length_b	52.171 Å
length_c	52.337 Å
angle_alpha	90.00 °
angle_beta	102.23 °
angle_gamma	90.00 °
z_pdb	2

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

Refinement

resolution	1.830 Å
resolution_low	36.520 Å
r_factor	0.2001
r_work	0.1958
r_free	0.2388

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/ye/9yea/pr_distribution.json
• pr_output /app/data/pr_computation/ye/9yea/9yea.pr.out
• pr_plot /app/data/visualization/pr_computation/ye/9yea/9yea_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/ye/9yea/9yea.dat
• saxs_fit /app/data/saxs_computation/ye/9yea/9yea.fit
• saxs_log /app/data/saxs_computation/ye/9yea/9yea.log
• saxs_plot /app/data/visualization/saxs_computation/ye/9yea/9yea_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/ye/9yea/9yea.fit
pddf	/app/data/pr_computation/ye/9yea/9yea.pr.out
profile	/app/data/saxs_computation/ye/9yea/9yea.dat