perdeuterated human DJ-1, 100K

Method: X-RAY DIFFRACTION D_max: 52.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yfr
deposition_date	2025-09-26
title	perdeuterated 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	17.99 Å
rg_electron	15.28 Å
i0	2140040.00
molecular_weight	22812.0 kDa
excluded_volume	33183 Å³
envelope_volume	31960 Å³
shell_volume	16507 Å³
envelope_diameter	51.9 Å
shell_rg	22.39 Å
envelope_rg	16.25 Å
shape_rg	15.26 Å
total_rg	17.88 Å
total_atoms	2845
n_residues	188
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	52.1 Å
rg_real	17.82 Å
rg_real_error	0.27 Å
i0_real	2.1400e+06
i0_real_error	2.2470e+04
rg_reciprocal	17.84 Å
i0_reciprocal	2140000.0000
total_estimate	0.8329
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.0 Å
skewness	-0.075
kurtosis	-0.386
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	427300.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.644

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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	74.836 Å
length_b	74.836 Å
length_c	75.347 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	0.920 Å
resolution_low	37.420 Å
r_factor	0.1041
r_work	0.1039
r_free	0.1125

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	3718

perdeuterated 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	2

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	304

fit	/app/data/saxs_computation/yf/9yfr/9yfr.fit
pddf	/app/data/pr_computation/yf/9yfr/9yfr.pr.out
profile	/app/data/saxs_computation/yf/9yfr/9yfr.dat