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9v65

Cryo-EM structure of free-state VbAgo

Method: ELECTRON MICROSCOPY D_max: 87.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v65
deposition_date	2025-05-26
title	Cryo-EM structure of free-state VbAgo
keywords	mesophilic prokaryotic Argonaute, 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	29.04 Å
rg_electron	27.82 Å
i0	128338000.00
molecular_weight	87984.0 kDa
excluded_volume	109880 Å³
envelope_volume	143090 Å³
shell_volume	41712 Å³
envelope_diameter	90.1 Å
shell_rg	36.29 Å
envelope_rg	27.45 Å
shape_rg	27.81 Å
total_rg	28.71 Å
total_atoms	6209
n_residues	779
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	87.1 Å
rg_real	28.85 Å
rg_real_error	0.43 Å
i0_real	1.2830e+08
i0_real_error	1.7290e+06
rg_reciprocal	28.94 Å
i0_reciprocal	128300000.0000
total_estimate	0.9041
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	38.0 Å
skewness	0.100
kurtosis	-0.487
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	44250000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.955

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	VbAgo
formula_weight	88463.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6210

MSEKQLGATLFPITGLPAQAFRLRVLRVRETIPMDTQTPVRLNRWATQLWKELKQAVVPTGRFEWPAFLTPDVESLTVGRVLTVQDVPDREYSIEVIGETVEVNPASASSEELQLAGEMIKRAISDAFGRNSDKYWRKHWNLYFRLEPENLQDRRDRVFAYRGLKFSVVFLGDKPWLAADILTTYHGQHALSEYSSEQRQRELHFHVSERIEADDRAMFLRDNGKIKIPCRFVGSTGKTVTQYTFPINGGQKNVREYYEQRYGIRVPENDEAVFVRDREGCDSWPVPASRLFPLFTTEYDEVRNCSVVPQMPPDERVETIRAFLNDLRDVSFAGSTLAIGHSHFQTAERSVFPAPALEFGNGQTLTVDASLPIEEGYNRYRQGKMTMLYEHGPFSSQSLPDLVLLYPDNLDRNAREKLRQRLGEEIKELCGVAPRIARQISYPLGKQPHAGAGLLAAADELVRNNDGTFLPVIVLADALREHIYDLLKRRLSSLASQCVRERTVARVARDEQAVGGSRLRNLALGILTAAGLQPWVLAKPLHYDFYMGVDLLANQVIYVFVCGKGGRNVWVQRGDQLRRRGITEKIDRVQLADQFKTGVREAKRLGVPLNSLVVHRDGRWWSNEDLAITEAVAELQGDGTLSKDCQVGVVEVRKSHLPVRLFSVLNATKGSLENPMPGSHLILNNTEAILTPTGQPGRWDKQGRTAGTLLLRITRNPNGSPLDIRKIAEDAYGLTHLNWNAPDIEISLPVTIRWSDERLREIVTNPSATDDTEVEPQETCIV

Source

organism	Verrucomicrobiota bacterium
ncbi_taxonomy_id	2026799
host_organism	Escherichia coli

Entity 2 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	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	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	84950

fit	/app/data/saxs_computation/v6/9v65/9v65.fit
pddf	/app/data/pr_computation/v6/9v65/9v65.pr.out
profile	/app/data/saxs_computation/v6/9v65/9v65.dat

Cryo-EM structure of free-state VbAgo

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)