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9v6b

Neutron crystal structure of the oxidized form of b5R at pD 6.5

Method: NEUTRON DIFFRACTION D_max: 62.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v6b
deposition_date	2025-05-27
title	Neutron crystal structure of the oxidized form of b5R at pD 6.5
keywords	fatty acid synthesis, methemoglobin reduction, xenobiotic oxidation, antioxidant defense, OXIDOREDUCTASE; OXIDOREDUCTASE
method	NEUTRON 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	19.92 Å
rg_electron	18.67 Å
i0	15368900.00
molecular_weight	32735.0 kDa
excluded_volume	42120 Å³
envelope_volume	48534 Å³
shell_volume	21030 Å³
envelope_diameter	63.3 Å
shell_rg	25.64 Å
envelope_rg	19.07 Å
shape_rg	18.90 Å
total_rg	18.95 Å
total_atoms	4513
n_residues	272
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	62.7 Å
rg_real	19.77 Å
rg_real_error	0.31 Å
i0_real	1.5370e+07
i0_real_error	1.7030e+05
rg_reciprocal	19.79 Å
i0_reciprocal	15370000.0000
total_estimate	0.8986
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.6 Å
skewness	0.099
kurtosis	-0.493
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	2937000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	NADH-cytochrome b5 reductase 3
formula_weight	30872.7 kDa
ec_number	1.6.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6073

STPAITLENPDIKYPLRLIDKEVVNHDTRRFRFALPSPQHILGLPVGQHIYLSARIDGNLVIRPYTPVSSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIGDTIEFRGPNGLLVYQGKGKFAIRPDKKSSPVIKTVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLRPELEELRNEHSARFKLWYTVDRAPEAWDYSQGFVNEEMIRDHLPPPEEEPLVLMCGPPPMIQYACLPNLERVGHPKERCFAF

Source

organism	Sus scrofa
common_name	pig
ncbi_taxonomy_id	9823
host_organism	Escherichia coli

Entity 2 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	nat
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	465

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6. Citations (1)

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length_a	48.628 Å
length_b	72.233 Å
length_c	85.080 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.600 Å
resolution_low	16.440 Å
r_factor	0.1801
r_work	0.1789
r_free	0.2015

fit	/app/data/saxs_computation/v6/9v6b/9v6b.fit
pddf	/app/data/pr_computation/v6/9v6b/9v6b.pr.out
profile	/app/data/saxs_computation/v6/9v6b/9v6b.dat

Neutron crystal structure of the oxidized form of b5R at pD 6.5

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