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9s4r

diFe-Sulerythin_E126D O2-reacted

Method: X-RAY DIFFRACTION D_max: 83.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s4r
deposition_date	2025-07-28
last_revision	2026-06-10
title	diFe-Sulerythin_E126D O2-reacted
keywords	dioxygen activation, four-helix bundle, diiron, diferric-peroxo ligand, 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	25.13 Å
rg_electron	24.47 Å
i0	40608100.00
molecular_weight	48356.0 kDa
excluded_volume	60053 Å³
envelope_volume	75720 Å³
shell_volume	26126 Å³
envelope_diameter	86.6 Å
shell_rg	31.26 Å
envelope_rg	24.50 Å
shape_rg	24.45 Å
total_rg	25.32 Å
total_atoms	6670
n_residues	426
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	83.5 Å
rg_real	25.08 Å
rg_real_error	0.72 Å
i0_real	4.0610e+07
i0_real_error	5.9730e+05
rg_reciprocal	25.10 Å
i0_reciprocal	40610000.0000
total_estimate	0.8952
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.8 Å
skewness	0.241
kurtosis	-0.412
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	3619000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Sulerythrin
formula_weight	16198.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	6924

NMKDLKGTKTAENLKQGFIGESMANRRYLYFAKRADEEGYPEIAGLLRSIAEGETAHAFGHLDFIRQGGLTDPATDKPIGTLEQMIESAIAGETYEWTQMYPGFAKVAREEGFPEVAEWFETLARADKSHAEKFQNVLKQLKGGT

Source

organism	Sulfurisphaera tokodaii str. 7
ncbi_taxonomy_id	273063
host_organism	Escherichia coli B

Entity 2 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	(R,R)-2,3-BUTANEDIOL
formula_weight	90.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	PEROXIDE ION
formula_weight	32.0 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	207

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6. Citations (1)

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length_a	100.480 Å
length_b	87.870 Å
length_c	59.730 Å
angle_alpha	90.00 °
angle_beta	115.85 °
angle_gamma	90.00 °
z_pdb	12

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.750 Å
resolution_low	34.020 Å
r_factor	0.1874
r_work	0.1853
r_free	0.2284

fit	/app/data/saxs_computation/s4/9s4r/9s4r.fit
pddf	/app/data/pr_computation/s4/9s4r/9s4r.pr.out
profile	/app/data/saxs_computation/s4/9s4r/9s4r.dat