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9sih

XFEL structure of Ribonucleotide reductase R2a Y122F mutant from E. coli,reduced form

Method: X-RAY DIFFRACTION D_max: 84.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sih
deposition_date	2025-08-28
title	XFEL structure of Ribonucleotide reductase R2a Y122F mutant from E. coli,reduced form
keywords	Ribonucleotide reductase beta subunit, R2a, Di-iron beta subunit, Reduced R2a, XFEL structure, 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	27.19 Å
rg_electron	26.00 Å
i0	98881600.00
molecular_weight	79294.0 kDa
excluded_volume	99476 Å³
envelope_volume	113780 Å³
shell_volume	35620 Å³
envelope_diameter	88.2 Å
shell_rg	34.49 Å
envelope_rg	26.20 Å
shape_rg	25.99 Å
total_rg	26.85 Å
total_atoms	5581
n_residues	681
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	84.3 Å
rg_real	27.09 Å
rg_real_error	0.50 Å
i0_real	9.8880e+07
i0_real_error	1.3880e+06
rg_reciprocal	27.13 Å
i0_reciprocal	98880000.0000
total_estimate	0.9023
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.0 Å
skewness	0.258
kurtosis	-0.438
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	27510000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ribonucleoside-diphosphate reductase 1 subunit beta
formula_weight	43410.9 kDa
ec_number	1.17.4.1
mutation	Y122F
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6068

AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSFTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDNVQVAPQEVEVSSYLVGQIDSEVDTDDLSNFQL

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	362

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6. Citations (1)

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length_a	74.182 Å
length_b	76.446 Å
length_c	146.265 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.700 Å
resolution_low	26.420 Å
r_factor	0.1587
r_work	0.1580
r_free	0.1905

fit	/app/data/saxs_computation/si/9sih/9sih.fit
pddf	/app/data/pr_computation/si/9sih/9sih.pr.out
profile	/app/data/saxs_computation/si/9sih/9sih.dat

XFEL structure of Ribonucleotide reductase R2a Y122F mutant from E. coli,reduced form

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