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9sk1

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

Method: ELECTRON CRYSTALLOGRAPHY D_max: 84.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sk1
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 reduced (red) 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	27.17 Å
rg_electron	25.99 Å
i0	98785600.00
molecular_weight	79338.0 kDa
excluded_volume	99566 Å³
envelope_volume	113230 Å³
shell_volume	35493 Å³
envelope_diameter	88.0 Å
shell_rg	34.44 Å
envelope_rg	26.20 Å
shape_rg	25.98 Å
total_rg	26.84 Å
total_atoms	11055
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	27.07 Å
rg_real_error	0.43 Å
i0_real	9.8790e+07
i0_real_error	1.2580e+06
rg_reciprocal	27.10 Å
i0_reciprocal	98790000.0000
total_estimate	0.9016
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.0 Å
skewness	0.258
kurtosis	-0.433
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	27350000.0000
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: 0.923

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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	11906

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	291

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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	0.1967
r_work	0.1961
r_free	0.2216

resolution	1.80 Å
resolution_method	—
num_particles	—

fit	/app/data/saxs_computation/sk/9sk1/9sk1.fit
pddf	/app/data/pr_computation/sk/9sk1/9sk1.pr.out
profile	/app/data/saxs_computation/sk/9sk1/9sk1.dat

Serial electron diffraction (SerialED) structure of Y122F mutant Ribonucleotide reductase R2 from E. coli in its reduced (red) 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