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9t6u

Higher-dose (1332 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at cryogenic temperature

Method: X-RAY DIFFRACTION D_max: 75.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t6u
deposition_date	2025-11-07
title	Higher-dose (1332 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at cryogenic 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	21.76 Å
rg_electron	20.58 Å
i0	24812400.00
molecular_weight	36985.0 kDa
excluded_volume	45755 Å³
envelope_volume	54509 Å³
shell_volume	22057 Å³
envelope_diameter	80.2 Å
shell_rg	27.43 Å
envelope_rg	21.34 Å
shape_rg	20.53 Å
total_rg	21.59 Å
total_atoms	2594
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	75.6 Å
rg_real	21.73 Å
rg_real_error	0.48 Å
i0_real	2.4810e+07
i0_real_error	3.2660e+05
rg_reciprocal	21.73 Å
i0_reciprocal	24810000.0000
total_estimate	0.7138
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.8 Å
skewness	0.345
kurtosis	-0.242
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	5431000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 0.348; Positv: 1.000; Valcen: 0.958; Smooth: 0.995

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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	3031

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	7

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	386

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6. Citations (1)

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length_a	95.375 Å
length_b	95.375 Å
length_c	95.375 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	1.500 Å
resolution_low	28.757 Å
r_factor	—
r_work	0.1535
r_free	0.1877

fit	/app/data/saxs_computation/t6/9t6u/9t6u.fit
pddf	/app/data/pr_computation/t6/9t6u/9t6u.pr.out
profile	/app/data/saxs_computation/t6/9t6u/9t6u.dat

Higher-dose (1332 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at cryogenic 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