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13sk

PanDDA analysis group deposition -- IDOL RING domain in complex with Z2692078340

Method: X-RAY DIFFRACTION D_max: 66.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13sk
deposition_date	2025-10-10
last_revision	2025-12-10
title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z2692078340
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	21.50 Å
rg_electron	20.56 Å
i0	22591100.00
molecular_weight	32699.0 kDa
excluded_volume	39495 Å³
envelope_volume	50583 Å³
shell_volume	20582 Å³
envelope_diameter	68.4 Å
shell_rg	26.90 Å
envelope_rg	20.66 Å
shape_rg	20.57 Å
total_rg	21.35 Å
total_atoms	2220
n_residues	276
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	66.7 Å
rg_real	21.37 Å
rg_real_error	0.40 Å
i0_real	2.2590e+07
i0_real_error	2.6590e+05
rg_reciprocal	21.40 Å
i0_reciprocal	22590000.0000
total_estimate	0.9094
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	64.7 Å
skewness	0.116
kurtosis	-0.475
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	1669000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.996

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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	2685

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	N-methyl-1-(1-phenyl-1H-pyrazol-4-yl)methanamine
formula_weight	187.2 kDa
src_method	syn
entity_count	4

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	264

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6. Citations (1)

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length_a	45.002 Å
length_b	48.146 Å
length_c	70.218 Å
angle_alpha	90.00 °
angle_beta	90.62 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.536 Å
resolution_low	39.710 Å
r_factor	0.1977
r_work	0.1961
r_free	0.2296

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