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13rz

PanDDA analysis group deposition -- IDOL RING domain in complex with Z1118527729

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13rz
deposition_date	2025-10-10
last_revision	2025-12-10
title	PanDDA analysis group deposition -- IDOL RING domain in complex with Z1118527729
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	21.40 Å
rg_electron	20.50 Å
i0	39304000.00
molecular_weight	30389.0 kDa
excluded_volume	28225 Å³
envelope_volume	50319 Å³
shell_volume	20492 Å³
envelope_diameter	68.3 Å
shell_rg	26.98 Å
envelope_rg	20.62 Å
shape_rg	20.55 Å
total_rg	21.06 Å
total_atoms	2211
n_residues	277
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	66.3 Å
rg_real	21.27 Å
rg_real_error	0.32 Å
i0_real	3.9300e+07
i0_real_error	4.3710e+05
rg_reciprocal	21.30 Å
i0_reciprocal	39300000.0000
total_estimate	0.7423
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	28.3 Å
skewness	0.110
kurtosis	-0.490
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	2499000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 0.281; Positv: 1.000; Valcen: 0.998; Smooth: 0.988

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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	2657

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	2-{[(1R,2R)-2-methylcyclopentyl]amino}ethan-1-ol
formula_weight	143.2 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	258

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6. Citations (1)

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length_a	44.540 Å
length_b	48.100 Å
length_c	70.450 Å
angle_alpha	90.00 °
angle_beta	90.81 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.660 Å
resolution_low	22.760 Å
r_factor	0.2017
r_work	0.2004
r_free	0.2287

fit	/app/data/saxs_computation/3r/13rz/13rz.fit
pddf	/app/data/pr_computation/3r/13rz/13rz.pr.out
profile	/app/data/saxs_computation/3r/13rz/13rz.dat