Crystal structure of class Ie ribonucleotide reductase R2 subunit from Mesoplasma florum with a D212N mutation

Method: X-RAY DIFFRACTION D_max: 82.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9r5l
deposition_date	2025-05-09
last_revision	2026-05-20
title	Crystal structure of class Ie ribonucleotide reductase R2 subunit from Mesoplasma florum with a D212N mutation
keywords	Ribonucleotide reductase R2e, Class Ie RNR, OXIDOREDUCTASE, ferritin-like superfamily, NrdF, RNR beta-subunit; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	22.22 Å
rg_electron	21.18 Å
i0	20437700.00
molecular_weight	35870.0 kDa
excluded_volume	45453 Å³
envelope_volume	52913 Å³
shell_volume	21370 Å³
envelope_diameter	85.7 Å
shell_rg	27.31 Å
envelope_rg	22.09 Å
shape_rg	21.12 Å
total_rg	22.19 Å
total_atoms	2539
n_residues	310
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

▼

3. P(r) Analysis (GNOM)

dmax	82.8 Å
rg_real	22.31 Å
rg_real_error	0.77 Å
i0_real	2.0440e+07
i0_real_error	3.0370e+05
rg_reciprocal	22.29 Å
i0_reciprocal	20440000.0000
total_estimate	0.8112
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.9 Å
skewness	0.528
kurtosis	0.108
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	3813000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.583; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.799; Smooth: 0.994

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

length_a	141.083 Å
length_b	45.774 Å
length_c	56.833 Å
angle_alpha	90.00 °
angle_beta	112.22 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.700 Å
resolution_low	43.200 Å
r_factor	0.2133
r_work	0.2111
r_free	0.2567

description	ribonucleoside-diphosphate reductase
formula_weight	39827.6 kDa
ec_number	1.17.4.1
mutation	D212N
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2778

Crystal structure of class Ie ribonucleotide reductase R2 subunit from Mesoplasma florum with a D212N mutation

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Mesoplasma florum L1
ncbi_taxonomy_id	265311
host_organism	Escherichia coli BL21(DE3)

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	179

fit	/app/data/saxs_computation/r5/9r5l/9r5l.fit
pddf	/app/data/pr_computation/r5/9r5l/9r5l.pr.out
profile	/app/data/saxs_computation/r5/9r5l/9r5l.dat