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9t6o

Low-dose (14.9 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at room temperature

Method: X-RAY DIFFRACTION D_max: 75.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t6o
deposition_date	2025-11-07
title	Low-dose (14.9 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at room temperature
keywords	NIR, CU-NIR, Radiation Damage, Nitrite metabolism, Room-temperature crystallography, Metalloproteins, 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	21.51 Å
rg_electron	20.48 Å
i0	22875800.00
molecular_weight	36144.0 kDa
excluded_volume	45053 Å³
envelope_volume	54040 Å³
shell_volume	21956 Å³
envelope_diameter	81.1 Å
shell_rg	27.31 Å
envelope_rg	21.28 Å
shape_rg	20.46 Å
total_rg	21.44 Å
total_atoms	2546
n_residues	331
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	75.8 Å
rg_real	21.48 Å
rg_real_error	0.66 Å
i0_real	2.2880e+07
i0_real_error	2.9790e+05
rg_reciprocal	21.48 Å
i0_reciprocal	22880000.0000
total_estimate	0.7768
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.5 Å
skewness	0.357
kurtosis	-0.193
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	5457000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Copper-containing nitrite reductase
formula_weight	40818.2 kDa
ec_number	1.7.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2850

MTEQLQMTRRTMLAGAALAGAVAPLLHTAQAHAAGAAAAAGAAPVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYQDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM

Source

organism	Achromobacter cycloclastes
ncbi_taxonomy_id	223
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	166

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6. Citations (1)

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length_a	96.472 Å
length_b	96.472 Å
length_c	96.472 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 3
int_tables_number	198
crystal_system	—

resolution	1.597 Å
resolution_low	27.865 Å
r_factor	—
r_work	0.1493
r_free	0.1790

fit	/app/data/saxs_computation/t6/9t6o/9t6o.fit
pddf	/app/data/pr_computation/t6/9t6o/9t6o.pr.out
profile	/app/data/saxs_computation/t6/9t6o/9t6o.dat

Low-dose (14.9 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at room temperature

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