Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)

Method: ELECTRON MICROSCOPY D_max: 110.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x6b
deposition_date	2025-10-15
title	Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
keywords	;Azoarcus sp. BH72 pre-tRNA(ILE); second-step cyclization; c' intron, RNA ;; RNA
method	ELECTRON MICROSCOPY

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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	30.95 Å
rg_electron	30.96 Å
i0	203973000.00
molecular_weight	65568.0 kDa
excluded_volume	60974 Å³
envelope_volume	101310 Å³
shell_volume	29921 Å³
envelope_diameter	116.2 Å
shell_rg	34.74 Å
envelope_rg	30.60 Å
shape_rg	30.91 Å
total_rg	31.24 Å
total_atoms	4325
n_residues	201
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	110.0 Å
rg_real	31.12 Å
rg_real_error	1.07 Å
i0_real	2.0400e+08
i0_real_error	3.3990e+06
rg_reciprocal	31.05 Å
i0_reciprocal	204000000.0000
total_estimate	0.8527
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.7 Å
skewness	0.517
kurtosis	0.021
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	5150000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.868; Smooth: 0.954

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.86 Å
resolution_method	—
num_particles	213341

description	Azoarcus sp. BH72 self-splicing group I intron of tRNA-Ile
formula_weight	65174.0 kDa
src_method	man
entity_count	1

type	polyribonucleotide
strand_id	B
atom_count	4325

Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular 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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Azoarcus olearius
ncbi_taxonomy_id	418699
host_organism	in vitro transcription vector pT7-Fluc(deltai)

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

fit	/app/data/saxs_computation/x6/9x6b/9x6b.fit
pddf	/app/data/pr_computation/x6/9x6b/9x6b.pr.out
profile	/app/data/saxs_computation/x6/9x6b/9x6b.dat