Apo-form of Schistosoma mansoni Cathepsin D1 at 2.2A resolution

Method: X-RAY DIFFRACTION D_max: 66.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9snt
deposition_date	2025-09-11
last_revision	2026-02-18
title	Apo-form of Schistosoma mansoni Cathepsin D1 at 2.2A resolution
keywords	Apo-form, Cathepsin D, lysosomal aspartyl protease, 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	21.11 Å
rg_electron	19.92 Å
i0	24265100.00
molecular_weight	39711.0 kDa
excluded_volume	50479 Å³
envelope_volume	56324 Å³
shell_volume	23224 Å³
envelope_diameter	66.9 Å
shell_rg	26.80 Å
envelope_rg	20.01 Å
shape_rg	19.89 Å
total_rg	20.92 Å
total_atoms	2795
n_residues	362
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	66.0 Å
rg_real	20.99 Å
rg_real_error	0.35 Å
i0_real	2.4270e+07
i0_real_error	3.5270e+05
rg_reciprocal	21.01 Å
i0_reciprocal	24270000.0000
total_estimate	0.7537
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.184
kurtosis	-0.423
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	5737000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.993; Smooth: 0.979

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	136.617 Å
length_b	136.617 Å
length_c	51.803 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 62
int_tables_number	171
crystal_system	hexagonal

resolution	2.200 Å
resolution_low	47.450 Å
r_factor	0.1760
r_work	0.1741
r_free	0.2008

description	Cathepsin D (A01 family)
formula_weight	47001.1 kDa
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2914

Apo-form of Schistosoma mansoni Cathepsin D1 at 2.2A resolution

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Schistosoma mansoni
ncbi_taxonomy_id	6183
host_organism	Homo sapiens

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	119

fit	/app/data/saxs_computation/sn/9snt/9snt.fit
pddf	/app/data/pr_computation/sn/9snt/9snt.pr.out
profile	/app/data/saxs_computation/sn/9snt/9snt.dat