Cryo-EM strucutre of the apo Mucilaginibacter paludis Argonaute

Method: ELECTRON MICROSCOPY D_max: 101.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wmd
deposition_date	2025-09-03
title	Cryo-EM strucutre of the apo Mucilaginibacter paludis Argonaute
keywords	Mucilaginibacter paludis Argonaute, apo-state structure, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	29.89 Å
rg_electron	28.72 Å
i0	106049000.00
molecular_weight	85312.0 kDa
excluded_volume	108620 Å³
envelope_volume	138730 Å³
shell_volume	39839 Å³
envelope_diameter	105.9 Å
shell_rg	36.57 Å
envelope_rg	28.29 Å
shape_rg	28.71 Å
total_rg	29.57 Å
total_atoms	6036
n_residues	741
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	101.3 Å
rg_real	29.76 Å
rg_real_error	0.90 Å
i0_real	1.0600e+08
i0_real_error	1.7340e+06
rg_reciprocal	29.81 Å
i0_reciprocal	106100000.0000
total_estimate	0.7976
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.2 Å
skewness	0.219
kurtosis	-0.282
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	23350000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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	3.590 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.59 Å
resolution_method	—
num_particles	347888

description	Piwi domain-containing protein
formula_weight	93827.4 kDa
src_method	man
entity_count	1

Cryo-EM strucutre of the apo Mucilaginibacter paludis Argonaute

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	Mucilaginibacter paludis DSM 18603
ncbi_taxonomy_id	714943
host_organism	Escherichia coli

fit	/app/data/saxs_computation/wm/9wmd/9wmd.fit
pddf	/app/data/pr_computation/wm/9wmd/9wmd.pr.out
profile	/app/data/saxs_computation/wm/9wmd/9wmd.dat

type	polypeptide(L)
strand_id	A
atom_count	6036