Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 9

Method: ELECTRON MICROSCOPY D_max: 158.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zgr
deposition_date	2025-12-03
title	Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 9
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	45.79 Å
rg_electron	46.06 Å
i0	848441000.00
molecular_weight	136940.0 kDa
excluded_volume	127310 Å³
envelope_volume	234090 Å³
shell_volume	46047 Å³
envelope_diameter	163.0 Å
shell_rg	46.20 Å
envelope_rg	44.38 Å
shape_rg	46.05 Å
total_rg	46.07 Å
total_atoms	9010
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	158.4 Å
rg_real	46.05 Å
rg_real_error	1.52 Å
i0_real	8.4840e+08
i0_real_error	1.6820e+07
rg_reciprocal	45.80 Å
i0_reciprocal	848200000.0000
total_estimate	0.8741
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.9 Å
skewness	0.397
kurtosis	-0.446
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0002
highest_alpha	19440000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.810

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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	2.930 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.93 Å
resolution_method	—
num_particles	76728

description	RNase P RNA
formula_weight	135304.2 kDa
src_method	man
entity_count	1

Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 9

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	48

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

type	polyribonucleotide
strand_id	A
atom_count	9010