← Back to search

13sr

PanDDA analysis group deposition -- IDOL RING domain in complex with Z48852953

Method: X-RAY DIFFRACTION D_max: 66.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	13sr
deposition_date	2025-10-10
last_revision	2025-12-10
title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z48852953
keywords	Diamond I04-1 fragment screening, PanDDA, XChemExplorer, E3, ubiquitin, Zinc finger, RING, ligase; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	21.07 Å
rg_electron	20.15 Å
i0	42321800.00
molecular_weight	31516.0 kDa
excluded_volume	29244 Å³
envelope_volume	50986 Å³
shell_volume	21044 Å³
envelope_diameter	68.5 Å
shell_rg	26.67 Å
envelope_rg	20.49 Å
shape_rg	20.19 Å
total_rg	20.73 Å
total_atoms	2293
n_residues	290
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	66.3 Å
rg_real	20.96 Å
rg_real_error	0.34 Å
i0_real	4.2320e+07
i0_real_error	4.5350e+05
rg_reciprocal	20.98 Å
i0_reciprocal	42320000.0000
total_estimate	0.9037
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.3 Å
skewness	0.160
kurtosis	-0.441
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	3415000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	E3 ubiquitin-protein ligase MYLIP
formula_weight	8820.4 kDa
ec_number	2.3.2.27
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	2634

SQQTRVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTSLLNLTVI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	4-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1,3-thiazol-2-amine
formula_weight	198.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	165

▶

6. Citations (1)

▶

length_a	44.640 Å
length_b	47.730 Å
length_c	69.940 Å
angle_alpha	90.00 °
angle_beta	90.78 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.650 Å
resolution_low	22.320 Å
r_factor	0.2033
r_work	0.2020
r_free	0.2302

fit	/app/data/saxs_computation/3s/13sr/13sr.fit
pddf	/app/data/pr_computation/3s/13sr/13sr.pr.out
profile	/app/data/saxs_computation/3s/13sr/13sr.dat