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9rll

;Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX) ;

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	9rll
deposition_date	2025-06-16
title	;Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX) ;
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	21.80 Å
rg_electron	20.62 Å
i0	24985000.00
molecular_weight	37085.0 kDa
excluded_volume	45896 Å³
envelope_volume	54521 Å³
shell_volume	22067 Å³
envelope_diameter	80.7 Å
shell_rg	27.44 Å
envelope_rg	21.34 Å
shape_rg	20.58 Å
total_rg	21.64 Å
total_atoms	5092
n_residues	332
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	21.76 Å
rg_real_error	0.47 Å
i0_real	2.4980e+07
i0_real_error	3.2520e+05
rg_reciprocal	21.77 Å
i0_reciprocal	24990000.0000
total_estimate	0.7876
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.9 Å
skewness	0.345
kurtosis	-0.242
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	5498000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; 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	36620.3 kDa
ec_number	1.7.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5834

VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYQDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM

Source

organism	Achromobacter cycloclastes
ncbi_taxonomy_id	223
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	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	501

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6. Citations (1)

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length_a	95.250 Å
length_b	95.250 Å
length_c	95.250 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	0.950 Å
resolution_low	16.844 Å
r_factor	—
r_work	0.1344
r_free	0.1605

fit	/app/data/saxs_computation/rl/9rll/9rll.fit
pddf	/app/data/pr_computation/rl/9rll/9rll.pr.out
profile	/app/data/saxs_computation/rl/9rll/9rll.dat

;Sub-atomic resolution (0.95 A) XFEL structure of as-isolated copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography (SF-ROX) ;

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