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9wzl

Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domain

Method: X-RAY DIFFRACTION D_max: 134.5 Å Quality: SUSPICIOUS

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wzl
deposition_date	2025-09-29
title	Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domain
keywords	endosperm, PLANT PROTEIN; PLANT PROTEIN
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	41.73 Å
rg_electron	42.49 Å
i0	45394800.00
molecular_weight	55981.0 kDa
excluded_volume	70756 Å³
envelope_volume	103340 Å³
shell_volume	23761 Å³
envelope_diameter	146.7 Å
shell_rg	39.16 Å
envelope_rg	42.29 Å
shape_rg	42.49 Å
total_rg	42.30 Å
total_atoms	3946
n_residues	511
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	134.5 Å
rg_real	42.47 Å
rg_real_error	1.82 Å
i0_real	4.5390e+07
i0_real_error	9.1930e+05
rg_reciprocal	41.74 Å
i0_reciprocal	45360000.0000
total_estimate	0.3910
solution_quality	SUSPICIOUS a SUSPICIOUS solution
n_peaks	2
r_peak_primary	21.2 Å
skewness	0.557
kurtosis	-0.646
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	1722000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.268; Stabil: 0.999; Sysdev: 0.046; Positv: 1.000; Valcen: 0.139; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Protein disulfide isomerase-like 2-3
formula_weight	32044.2 kDa
ec_number	5.3.4.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4300

GPLGSGGKKSGGSSEKTEPSASIELNSQNFDKLVTKSKDLWIVEFFAPWCGHCKKLAPEWKKAAKNLKGQVKLGHVDCDAEKSLMSKYKVEGFPTILVFGADKESPFPYQGARVASAIESFALEQLEANAAPPEVSELTGPDAMEEKCASAAICFVSFLPDILDSKAEGRNKYLELLLSVAEKFKKSPYSFVWTAAGKQADLEKQVGVGGYGYPAMVALNVKKGAYAPLRSAFQLDEITEFVREAGRGGKGNLPLDGTPTIVQSEPWDGKDGEVIEEDEFSLEELMADNSPVNDEL

Source

organism	Oryza sativa Japonica Group
common_name	Japanese rice
ncbi_taxonomy_id	39947
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	209.2 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	354

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6. Citations (1)

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length_a	33.724 Å
length_b	174.375 Å
length_c	53.015 Å
angle_alpha	90.00 °
angle_beta	103.08 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	32.281 Å
r_factor	—
r_work	0.1902
r_free	0.2528

fit	/app/data/saxs_computation/wz/9wzl/9wzl.fit
pddf	/app/data/pr_computation/wz/9wzl/9wzl.pr.out
profile	/app/data/saxs_computation/wz/9wzl/9wzl.dat

Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domain

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