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13si

PanDDA analysis group deposition -- IDOL RING domain in complex with Z2574937229

Method: X-RAY DIFFRACTION D_max: 72.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13si
deposition_date	2025-10-10
last_revision	2025-12-10
title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z2574937229
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	21.62 Å
rg_electron	20.67 Å
i0	22913900.00
molecular_weight	33386.0 kDa
excluded_volume	40535 Å³
envelope_volume	51835 Å³
shell_volume	20966 Å³
envelope_diameter	68.5 Å
shell_rg	27.25 Å
envelope_rg	20.71 Å
shape_rg	20.68 Å
total_rg	21.50 Å
total_atoms	2267
n_residues	281
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	72.8 Å
rg_real	21.49 Å
rg_real_error	0.54 Å
i0_real	2.2910e+07
i0_real_error	3.3050e+05
rg_reciprocal	21.52 Å
i0_reciprocal	22910000.0000
total_estimate	0.8090
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.8 Å
skewness	0.109
kurtosis	-0.497
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	1840000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	2719

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	(S)-1-(4-methoxyphenyl)-1-phenylmethanamine
formula_weight	213.3 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	288

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6. Citations (1)

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length_a	44.849 Å
length_b	48.026 Å
length_c	70.560 Å
angle_alpha	90.00 °
angle_beta	90.90 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.540 Å
resolution_low	29.860 Å
r_factor	0.1818
r_work	0.1803
r_free	0.2113

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