← Back to search

13sa

PanDDA analysis group deposition -- IDOL RING domain in complex with Z1251361039

Method: X-RAY DIFFRACTION D_max: 65.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	13sa
deposition_date	2025-10-10
last_revision	2025-12-10
title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z1251361039
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	21.30 Å
rg_electron	20.38 Å
i0	40370900.00
molecular_weight	30643.0 kDa
excluded_volume	28385 Å³
envelope_volume	50713 Å³
shell_volume	20802 Å³
envelope_diameter	68.6 Å
shell_rg	26.79 Å
envelope_rg	20.64 Å
shape_rg	20.43 Å
total_rg	20.95 Å
total_atoms	2227
n_residues	282
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	65.9 Å
rg_real	21.18 Å
rg_real_error	0.46 Å
i0_real	4.0370e+07
i0_real_error	5.2050e+05
rg_reciprocal	21.21 Å
i0_reciprocal	40370000.0000
total_estimate	0.8302
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.1 Å
skewness	0.141
kurtosis	-0.460
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	3095000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

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	2606

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	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	(2R)-2-hydroxy-N-[(Z)-(pyridin-2-yl)methylidene]propanamide
formula_weight	178.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	185

▶

6. Citations (1)

▶

length_a	44.718 Å
length_b	48.054 Å
length_c	70.644 Å
angle_alpha	90.00 °
angle_beta	90.85 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.569 Å
resolution_low	70.640 Å
r_factor	0.2015
r_work	0.1999
r_free	0.2341

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