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9ths

Room temperature structure of Ascorbate Peroxidase at 1.54A

Method: X-RAY DIFFRACTION D_max: 58.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ths
deposition_date	2025-12-03
title	Room temperature structure of Ascorbate Peroxidase at 1.54A
keywords	Ascorbate, Peroxidase, Room Temperature, Oxidoreductase; OXIDOREDUCTASE
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	18.22 Å
rg_electron	17.14 Å
i0	12955500.00
molecular_weight	27552.0 kDa
excluded_volume	34658 Å³
envelope_volume	38403 Å³
shell_volume	18421 Å³
envelope_diameter	58.2 Å
shell_rg	23.62 Å
envelope_rg	17.41 Å
shape_rg	17.11 Å
total_rg	18.20 Å
total_atoms	3849
n_residues	249
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	58.2 Å
rg_real	18.11 Å
rg_real_error	0.28 Å
i0_real	1.2960e+07
i0_real_error	1.4460e+05
rg_reciprocal	18.13 Å
i0_reciprocal	12960000.0000
total_estimate	0.8856
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.144
kurtosis	-0.366
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	4459000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ascorbate peroxidase
formula_weight	26956.4 kDa
ec_number	1.11.1.11
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3966

GKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA

Source

organism	Glycine max
common_name	soybean
ncbi_taxonomy_id	3847
host_organism	Escherichia coli

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	101

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6. Citations (1)

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length_a	82.831 Å
length_b	82.831 Å
length_c	76.017 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 42 21 2
int_tables_number	94
crystal_system	—

resolution	1.540 Å
resolution_low	28.019 Å
r_factor	—
r_work	0.1667
r_free	0.2013

fit	/app/data/saxs_computation/th/9ths/9ths.fit
pddf	/app/data/pr_computation/th/9ths/9ths.pr.out
profile	/app/data/saxs_computation/th/9ths/9ths.dat

Room temperature structure of Ascorbate Peroxidase at 1.54A

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