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9sjw

;Serial electron diffraction (SerialED) structure of Y122F mutant Ribonucleotide reductase R2 from E. coli in its oxidised (met) form ;

Method: ELECTRON CRYSTALLOGRAPHY D_max: 87.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sjw
deposition_date	2025-09-01
last_revision	2026-04-22
title	;Serial electron diffraction (SerialED) structure of Y122F mutant Ribonucleotide reductase R2 from E. coli in its oxidised (met) form ;
keywords	;serial electron diffraction, SerialED, microcrystal, metalloenzyme, iron, ribonucleotide reductase, electrostatic potential, OXIDOREDUCTASE ;; OXIDOREDUCTASE
method	ELECTRON CRYSTALLOGRAPHY

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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	27.27 Å
rg_electron	26.06 Å
i0	99002200.00
molecular_weight	79338.0 kDa
excluded_volume	99566 Å³
envelope_volume	114660 Å³
shell_volume	35766 Å³
envelope_diameter	88.3 Å
shell_rg	34.59 Å
envelope_rg	26.31 Å
shape_rg	26.05 Å
total_rg	26.92 Å
total_atoms	11052
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	87.4 Å
rg_real	27.18 Å
rg_real_error	0.48 Å
i0_real	9.9000e+07
i0_real_error	1.5380e+06
rg_reciprocal	27.21 Å
i0_reciprocal	99000000.0000
total_estimate	0.8967
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	31.6 Å
skewness	0.267
kurtosis	-0.416
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	30310000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.968

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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
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	11869

AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSFTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDNVQVAPQEVEVSSYLVGQIDSEVDTDDLSNFQL

Source

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

Entity 2 non-polymer

description	FE (III) 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	420

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6. Citations (1)

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length_a	73.950 Å
length_b	76.540 Å
length_c	145.740 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	1.800 Å
resolution_low	19.930 Å
r_factor	0.2016
r_work	0.2008
r_free	0.2338

resolution	1.80 Å
resolution_method	—
num_particles	—

fit	/app/data/saxs_computation/sj/9sjw/9sjw.fit
pddf	/app/data/pr_computation/sj/9sjw/9sjw.pr.out
profile	/app/data/saxs_computation/sj/9sjw/9sjw.dat

;Serial electron diffraction (SerialED) structure of Y122F mutant Ribonucleotide reductase R2 from E. coli in its oxidised (met) 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

EM 3D