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9ro1

;Atomic resolution (1.00 A) XFEL structure of as-isolated copper nitrite reductase from Bradyrhizobium sp. at high pH (7.3) determined by serial femtosecond rotation crystallography (SF-ROX) at 100 K ;

Method: X-RAY DIFFRACTION D_max: 83.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ro1
deposition_date	2025-06-19
title	;Atomic resolution (1.00 A) XFEL structure of as-isolated copper nitrite reductase from Bradyrhizobium sp. at high pH (7.3) determined by serial femtosecond rotation crystallography (SF-ROX) at 100 K ;
keywords	Copper-containing nitrite reductase, BrJNiR, 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	21.93 Å
rg_electron	20.99 Å
i0	24557600.00
molecular_weight	37182.0 kDa
excluded_volume	46231 Å³
envelope_volume	55444 Å³
shell_volume	22135 Å³
envelope_diameter	84.9 Å
shell_rg	27.59 Å
envelope_rg	22.15 Å
shape_rg	20.94 Å
total_rg	22.01 Å
total_atoms	5135
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	83.5 Å
rg_real	21.97 Å
rg_real_error	0.70 Å
i0_real	2.4560e+07
i0_real_error	3.3700e+05
rg_reciprocal	21.96 Å
i0_reciprocal	24560000.0000
total_estimate	0.8026
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.9 Å
skewness	0.477
kurtosis	0.053
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	5792000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.556; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.771; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5976

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	alpha-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	484

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6. Citations (1)

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length_a	103.820 Å
length_b	103.820 Å
length_c	64.470 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	1.000 Å
resolution_low	16.765 Å
r_factor	—
r_work	0.1347
r_free	0.1566

fit	/app/data/saxs_computation/ro/9ro1/9ro1.fit
pddf	/app/data/pr_computation/ro/9ro1/9ro1.pr.out
profile	/app/data/saxs_computation/ro/9ro1/9ro1.dat