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9wiz

Structural Analysis of a Plant Glycoside Hydrolase Family 116 Glucosyl Ceramidase by Cryogenic Electron Microscopy (Cryo-EM)

Method: ELECTRON MICROSCOPY D_max: 160.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

P(r) distribution for 9wiz

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1. Structure Basics

entry_id	9wiz
deposition_date	2025-08-30
title	Structural Analysis of a Plant Glycoside Hydrolase Family 116 Glucosyl Ceramidase by Cryogenic Electron Microscopy (Cryo-EM)
keywords	Glucosylceramide, AtGCD3, plant, GH116, GBA2, glucosylceramidase, HYDROLASE; HYDROLASE
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	55.35 Å
rg_electron	54.49 Å
i0	5353770000.00
molecular_weight	621740.0 kDa
excluded_volume	778580 Å³
envelope_volume	1079200 Å³
shell_volume	154600 Å³
envelope_diameter	163.0 Å
shell_rg	65.52 Å
envelope_rg	52.65 Å
shape_rg	54.47 Å
total_rg	54.80 Å
total_atoms	43908
n_residues	5496
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	160.4 Å
rg_real	54.92 Å
rg_real_error	0.69 Å
i0_real	5.3540e+09
i0_real_error	9.3120e+07
rg_reciprocal	55.70 Å
i0_reciprocal	5360000000.0000
total_estimate	0.8542
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	74.5 Å
skewness	-0.048
kurtosis	-0.534
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0001
highest_alpha	711300000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.371

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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6. Citations (1)

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7. Files & Curves (10)