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9xj0

Crystal structure of SOD1 by serial synchrotron crystallography

Method: X-RAY DIFFRACTION D_max: 71.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xj0
deposition_date	2025-11-04
last_revision	2026-04-01
title	Crystal structure of SOD1 by serial synchrotron crystallography
keywords	hSOD1, SOD1, superoxide dismutase (Cu-Zn), 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	21.02 Å
rg_electron	20.05 Å
i0	20421300.00
molecular_weight	31855.0 kDa
excluded_volume	38855 Å³
envelope_volume	46342 Å³
shell_volume	19669 Å³
envelope_diameter	72.0 Å
shell_rg	26.18 Å
envelope_rg	20.35 Å
shape_rg	20.06 Å
total_rg	20.82 Å
total_atoms	2224
n_residues	306
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	71.4 Å
rg_real	21.02 Å
rg_real_error	0.46 Å
i0_real	2.0420e+07
i0_real_error	2.6580e+05
rg_reciprocal	21.02 Å
i0_reciprocal	20420000.0000
total_estimate	0.8801
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.8 Å
skewness	0.347
kurtosis	-0.366
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	2367000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Superoxide dismutase [Cu-Zn]
formula_weight	15827.6 kDa
ec_number	1.15.1.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2336

ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	24

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6. Citations (1)

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length_a	113.800 Å
length_b	113.800 Å
length_c	71.400 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63
int_tables_number	173
crystal_system	—

resolution	2.300 Å
resolution_low	98.550 Å
r_factor	0.1865
r_work	0.1852
r_free	0.2102

fit	/app/data/saxs_computation/xj/9xj0/9xj0.fit
pddf	/app/data/pr_computation/xj/9xj0/9xj0.pr.out
profile	/app/data/saxs_computation/xj/9xj0/9xj0.dat

Crystal structure of SOD1 by serial synchrotron crystallography

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