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9rnz

;Atomic resolution (1.02 A) XFEL structure of nitrite-bound copper nitrite reductase from Bradyrhizobium sp. determined by serial femtosecond rotation crystallography (SF-ROX) at 100 K ;

Method: X-RAY DIFFRACTION D_max: 83.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rnz
deposition_date	2025-06-19
title	;Atomic resolution (1.02 A) XFEL structure of nitrite-bound copper nitrite reductase from Bradyrhizobium sp. determined by serial femtosecond rotation crystallography (SF-ROX) at 100 K ;
keywords	Copper-containing nitrite reductase, AcNiR, SF-ROX, as-isolated, sub-atomic resolution, 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	21.87 Å
rg_electron	20.97 Å
i0	24530100.00
molecular_weight	37178.0 kDa
excluded_volume	46217 Å³
envelope_volume	55457 Å³
shell_volume	22147 Å³
envelope_diameter	86.3 Å
shell_rg	27.73 Å
envelope_rg	22.14 Å
shape_rg	20.92 Å
total_rg	21.99 Å
total_atoms	5137
n_residues	333
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	83.3 Å
rg_real	21.91 Å
rg_real_error	0.63 Å
i0_real	2.4530e+07
i0_real_error	3.1030e+05
rg_reciprocal	21.90 Å
i0_reciprocal	24530000.0000
total_estimate	0.6192
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	24.9 Å
skewness	0.478
kurtosis	0.049
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0001
highest_alpha	5970000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.553; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 0.772; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Copper-containing nitrite reductase
formula_weight	36928.9 kDa
ec_number	1.7.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5876

DDLKLPRQKVELVAPPFVHAHEQATKQGPKIVEFKLTIEEKKVVIDEKGTTFQAMTFNGSMPGPLMVVHEGDYVETTLVNPATNTMPHNIDFHSATGALGGGALTLINPGEQVVLRWKATKTGVFVYHCAPGGPMIPWHVVSGMNGAVMVLPRDGLNDGKGHALKYDKVYYVGEQDMYVPRDEKGNFKSYDSPGEAFTDTEEMMKKLIPSHVVFNGKVGALTGKNALTANVGENVLIVHSQANRDSRPHLIGGHGDYVWETGKFGNAPEVGLETWFIRGGSAGAAMYKFMQPGIYAYVTHNLIEAADLGATAHFKVEGKWNDDLMTQVKAPAEIPANTN

Source

organism	Bradyrhizobium diazoefficiens USDA 110
ncbi_taxonomy_id	224911
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	NITRITE ION
formula_weight	46.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	alpha-D-glucopyranose
formula_weight	180.2 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	beta-D-fructofuranose
formula_weight	180.2 kDa
src_method	man
entity_count	1

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	438

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6. Citations (1)

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length_a	103.890 Å
length_b	103.890 Å
length_c	64.350 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 63
int_tables_number	173
crystal_system	—

resolution	1.020 Å
resolution_low	16.765 Å
r_factor	—
r_work	0.1461
r_free	0.1607

fit	/app/data/saxs_computation/rn/9rnz/9rnz.fit
pddf	/app/data/pr_computation/rn/9rnz/9rnz.pr.out
profile	/app/data/saxs_computation/rn/9rnz/9rnz.dat