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13so

PanDDA analysis group deposition -- IDOL RING domain in complex with Z285233820

Method: X-RAY DIFFRACTION D_max: 66.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13so
deposition_date	2025-10-10
last_revision	2025-12-10
title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z285233820
keywords	Diamond I04-1 fragment screening, PanDDA, XChemExplorer, E3, ubiquitin, Zinc finger, RING, ligase; LIGASE
method	X-RAY DIFFRACTION

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	21.25 Å
rg_electron	20.30 Å
i0	22902700.00
molecular_weight	32711.0 kDa
excluded_volume	39438 Å³
envelope_volume	49633 Å³
shell_volume	20484 Å³
envelope_diameter	68.1 Å
shell_rg	26.62 Å
envelope_rg	20.54 Å
shape_rg	20.30 Å
total_rg	21.11 Å
total_atoms	2218
n_residues	280
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

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3. P(r) Analysis (GNOM)

dmax	66.4 Å
rg_real	21.13 Å
rg_real_error	0.35 Å
i0_real	2.2900e+07
i0_real_error	3.2310e+05
rg_reciprocal	21.16 Å
i0_reciprocal	22900000.0000
total_estimate	0.9076
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.4 Å
skewness	0.151
kurtosis	-0.456
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	2055000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.992

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4. Crystallography & Experiment

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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	2632

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	(5M)-5-(2-methoxyphenyl)-1,3,4-oxadiazol-2-amine
formula_weight	191.2 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	230

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6. Citations (1)

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length_a	44.499 Å
length_b	47.688 Å
length_c	70.287 Å
angle_alpha	90.00 °
angle_beta	90.74 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.615 Å
resolution_low	44.490 Å
r_factor	0.1961
r_work	0.1946
r_free	0.2260

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