Protiated human DJ-1, 100K

Method: X-RAY DIFFRACTION D_max: 50.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ycu
deposition_date	2025-09-19
title	Protiated human DJ-1, 100K
keywords	PARK7, glyoxalase, cyclic phosphoglycerate anhydride hydrolase, HYDROLASE; HYDROLASE
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	16.75 Å
rg_electron	15.35 Å
i0	7529370.00
molecular_weight	20121.0 kDa
excluded_volume	25356 Å³
envelope_volume	28476 Å³
shell_volume	15308 Å³
envelope_diameter	50.0 Å
shell_rg	21.65 Å
envelope_rg	15.76 Å
shape_rg	15.33 Å
total_rg	16.56 Å
total_atoms	2876
n_residues	189
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	50.6 Å
rg_real	16.61 Å
rg_real_error	0.24 Å
i0_real	7.5290e+06
i0_real_error	8.7960e+04
rg_reciprocal	16.63 Å
i0_reciprocal	7529000.0000
total_estimate	0.8997
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.4 Å
skewness	0.045
kurtosis	-0.469
angular_range	— – 0.4750 Å⁻¹
current_alpha	0.0000
highest_alpha	1597000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (2)

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length_a	75.109 Å
length_b	75.109 Å
length_c	75.505 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	1.050 Å
resolution_low	37.550 Å
r_factor	0.1187
r_work	0.1182
r_free	0.1342

description	Protein deglycase DJ-1
formula_weight	20199.3 kDa
ec_number	3.1.2.-,3.5.1.-
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	3661

Protiated human DJ-1, 100K

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	299

fit	/app/data/saxs_computation/yc/9ycu/9ycu.fit
pddf	/app/data/pr_computation/yc/9ycu/9ycu.pr.out
profile	/app/data/saxs_computation/yc/9ycu/9ycu.dat