Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 8

Method: ELECTRON MICROSCOPY D_max: 160.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zgq
deposition_date	2025-12-03
title	Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 8
keywords	RNase P RNA, Geobacillus stearothermophilus, catalytic RNA, cryo-EM structure, conformational heterogeneity, 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	46.15 Å
rg_electron	46.42 Å
i0	847088000.00
molecular_weight	136790.0 kDa
excluded_volume	127190 Å³
envelope_volume	238490 Å³
shell_volume	46350 Å³
envelope_diameter	160.6 Å
shell_rg	46.41 Å
envelope_rg	44.89 Å
shape_rg	46.41 Å
total_rg	46.43 Å
total_atoms	9004
n_residues	417
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	160.4 Å
rg_real	46.41 Å
rg_real_error	1.82 Å
i0_real	8.4710e+08
i0_real_error	1.5750e+07
rg_reciprocal	46.15 Å
i0_reciprocal	846800000.0000
total_estimate	0.8733
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.5 Å
skewness	0.392
kurtosis	-0.482
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	20820000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.838

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	73217

description	RNase P RNA
formula_weight	135305.2 kDa
src_method	man
entity_count	1

Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 8

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

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	Geobacillus stearothermophilus
ncbi_taxonomy_id	1422
host_organism	in vitro transcription vector pT7-TP(deltai)

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	42

fit	/app/data/saxs_computation/zg/9zgq/9zgq.fit
pddf	/app/data/pr_computation/zg/9zgq/9zgq.pr.out
profile	/app/data/saxs_computation/zg/9zgq/9zgq.dat

type	polyribonucleotide
strand_id	A
atom_count	9004