Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 3

Method: ELECTRON MICROSCOPY D_max: 162.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zfd
deposition_date	2025-12-01
title	Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 3
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	46.33 Å
rg_electron	46.70 Å
i0	846095000.00
molecular_weight	136650.0 kDa
excluded_volume	127050 Å³
envelope_volume	240430 Å³
shell_volume	46928 Å³
envelope_diameter	166.8 Å
shell_rg	46.09 Å
envelope_rg	45.58 Å
shape_rg	46.68 Å
total_rg	46.70 Å
total_atoms	8998
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	162.8 Å
rg_real	46.67 Å
rg_real_error	2.46 Å
i0_real	8.4610e+08
i0_real_error	1.7930e+07
rg_reciprocal	46.33 Å
i0_reciprocal	845700000.0000
total_estimate	0.8626
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.1 Å
skewness	0.450
kurtosis	-0.401
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	21140000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.833

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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	76672

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 3

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	36

fit	/app/data/saxs_computation/zf/9zfd/9zfd.fit
pddf	/app/data/pr_computation/zf/9zfd/9zfd.pr.out
profile	/app/data/saxs_computation/zf/9zfd/9zfd.dat

type	polyribonucleotide
strand_id	A
atom_count	8998