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9ygw

Perdeuterated E. coli YajL, 100K

Method: X-RAY DIFFRACTION D_max: 73.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ygw
deposition_date	2025-09-29
title	Perdeuterated E. coli YajL, 100K
keywords	DJ-1 superfamily, Cysteine dependent enzyme, 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	23.22 Å
rg_electron	20.68 Å
i0	7228930.00
molecular_weight	47399.0 kDa
excluded_volume	69032 Å³
envelope_volume	64511 Å³
shell_volume	25007 Å³
envelope_diameter	70.6 Å
shell_rg	28.27 Å
envelope_rg	21.40 Å
shape_rg	20.60 Å
total_rg	23.22 Å
total_atoms	5884
n_residues	390
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	73.1 Å
rg_real	23.12 Å
rg_real_error	0.53 Å
i0_real	7.2290e+06
i0_real_error	9.7550e+04
rg_reciprocal	23.14 Å
i0_reciprocal	7229000.0000
total_estimate	0.8866
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.1 Å
skewness	0.214
kurtosis	-0.326
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	2337000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Chaperone YajL
formula_weight	21080.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	7498

GSHMSASALVCLAPGSEETEAVTTIDLLVRGGIKVTTASVASDGNLAITCSRGVKLLADAPLVEVADGEYDVIVLPGGIKGAECFRDSTLLVETVKQFHRSGRIVAAICAAPATVLVPHDIFPIGNMTGFPTLKDKIPAEQWLDKRVVWDARVKLLTSQGPGTAIDFGLKIIDLLVGREKAHEVASQLVMAAGIYNYYE

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	642

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6. Citations (2)

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length_a	43.727 Å
length_b	78.410 Å
length_c	99.510 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	0.880 Å
resolution_low	39.200 Å
r_factor	0.1132
r_work	0.1128
r_free	0.1252

fit	/app/data/saxs_computation/yg/9ygw/9ygw.fit
pddf	/app/data/pr_computation/yg/9ygw/9ygw.pr.out
profile	/app/data/saxs_computation/yg/9ygw/9ygw.dat

Perdeuterated E. coli YajL, 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