MPNN-RFdiff designed RNA molecule

Method: ELECTRON MICROSCOPY D_max: 109.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11ag
deposition_date	2026-02-13
title	MPNN-RFdiff designed RNA molecule
keywords	pseudoknot, kissing multiloops, 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	32.69 Å
rg_electron	32.72 Å
i0	205180000.00
molecular_weight	65731.0 kDa
excluded_volume	61137 Å³
envelope_volume	108890 Å³
shell_volume	29972 Å³
envelope_diameter	114.0 Å
shell_rg	36.27 Å
envelope_rg	32.06 Å
shape_rg	32.67 Å
total_rg	32.98 Å
total_atoms	4338
n_residues	202
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	109.5 Å
rg_real	32.84 Å
rg_real_error	0.95 Å
i0_real	2.0520e+08
i0_real_error	3.1140e+06
rg_reciprocal	32.78 Å
i0_reciprocal	205200000.0000
total_estimate	0.8817
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.426
kurtosis	-0.249
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	8216000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.849

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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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	4.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.80 Å
resolution_method	—
num_particles	115837

description	RNA (518-MER)
formula_weight	167965.8 kDa
src_method	man
entity_count	2

MPNN-RFdiff designed RNA molecule

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia phage T7

fit	/app/data/saxs_computation/1a/11ag/11ag.fit
pddf	/app/data/pr_computation/1a/11ag/11ag.pr.out
profile	/app/data/saxs_computation/1a/11ag/11ag.dat

type	polyribonucleotide
strand_id	A,C
atom_count	4338