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9uxp

Local refinement of ITA bound OXGR1

Method: ELECTRON MICROSCOPY D_max: 74.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uxp
deposition_date	2025-05-14
title	Local refinement of ITA bound OXGR1
keywords	Itaconate acid, ITA, 2-oxoglutarate receptor 1, OXGR1, cryo-EM, membrane protein, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON MICROSCOPY

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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	21.59 Å
rg_electron	20.28 Å
i0	15692200.00
molecular_weight	32784.0 kDa
excluded_volume	42323 Å³
envelope_volume	47512 Å³
shell_volume	19999 Å³
envelope_diameter	75.4 Å
shell_rg	26.54 Å
envelope_rg	20.75 Å
shape_rg	20.23 Å
total_rg	21.41 Å
total_atoms	2307
n_residues	286
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	74.9 Å
rg_real	21.65 Å
rg_real_error	0.62 Å
i0_real	1.5690e+07
i0_real_error	2.0490e+05
rg_reciprocal	21.64 Å
i0_reciprocal	15690000.0000
total_estimate	0.8555
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.1 Å
skewness	0.420
kurtosis	-0.340
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	2652000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.905; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	2-oxoglutarate receptor 1
formula_weight	38284.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	2309

MNEPLDYLANASDFPDYAAAFGNCTDENIPLKMHYLPVIYGIIFLVGFPGNAVVISTYIFKMRPWKSSTIIMLNLACTDLLYLTSLPFLIHYYASGENWIFGDFMCKFIRFSFHFNLYSSILFLTCFSIFRYCVIIHPMSCFSIHKTRCAVVACAVVWIISLVAVIPMTFLITSTNRTNRSACLDLTSSDELNTIKWYNLILTATTFCLPLVIVTLCYTTIIHTLTHGLQTDSCLKQKARRLTILLLLAFYVCFLPFHILRVIRIESRLLSISCSIENQIHEAYIVSRPLAALNTFGNLLLYVVVSDNFQQAVCSTVRCKVSGNLEQAKKISYSNNP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	2-methylidenebutanedioic acid
formula_weight	130.1 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	405209

fit	/app/data/saxs_computation/ux/9uxp/9uxp.fit
pddf	/app/data/pr_computation/ux/9uxp/9uxp.pr.out
profile	/app/data/saxs_computation/ux/9uxp/9uxp.dat

Local refinement of ITA bound OXGR1

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

EM 3D