SAXSdb — 9s1f

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1. Structure Basics

entry_id	9s1f
deposition_date	2025-07-18
title	Cryo-EM structure of activated retron Eco2 (Ec67)
keywords	Retron, Reverse transcriptase, DNA, RNA, TOPRIM, RNaseH, msDNA, ANTIVIRAL PROTEIN; ANTIVIRAL 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	44.90 Å
rg_electron	45.29 Å
i0	1389620000.00
molecular_weight	266040.0 kDa
excluded_volume	314830 Å³
envelope_volume	450610 Å³
shell_volume	81385 Å³
envelope_diameter	136.2 Å
shell_rg	51.35 Å
envelope_rg	44.42 Å
shape_rg	45.29 Å
total_rg	45.52 Å
total_atoms	34918
n_residues	1927
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	142.7 Å
rg_real	44.66 Å
rg_real_error	1.02 Å
i0_real	1.3900e+09
i0_real_error	2.4070e+07
rg_reciprocal	44.90 Å
i0_reciprocal	1390000000.0000
total_estimate	0.8276
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	61.2 Å
skewness	0.082
kurtosis	-0.600
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0001
highest_alpha	190000000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	RNA (132-MER)
formula_weight	42593.2 kDa
src_method	man
entity_count	3

Polymer

type	polyribonucleotide
strand_id	D,E,F
atom_count	34918

CACGCAUGUAGGCAGAUUUGUUGGUUGUGAAUCGCAACCAGUGGCCUUAAUGGCAGGAGGAAUCGCCUCCCUAAAAUCCUUGAUUCAGAGCUAUACGGCAGGUGUGCUGUGCGAAGGAGUGCCUGCAUGCGU

Source

organism	Escherichia coli NCTC 86
ncbi_taxonomy_id	662541
host_organism	Escherichia coli DH5[alpha]

Entity 2 polymer

description	Retron Ec67 protein
formula_weight	68511.9 kDa
ec_number	2.7.7.49,3.1.26.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,A,C

MTKTSKLDALRAATSREDLAKILDVKLVFLTNVLYRIGSDNQYTQFTIPKKGKGVRTISAPTDRLKDIQRRICDLLSDCRDEIFAIRKISNNYSFGFERGKSIILNAYKHRGKQIILNIDLKDFFESFNFGRVRGYFLSNQDFLLNPVVATTLAKAACYNGTLPQGSPCSPIISNLICNIMDMRLAKLAKKYGCTYSRYADDITISTNKNTFPLEMATVQPEGVVLGKVLVKEIENSGFEINDSKTRLTYKTSRQEVTGLTVNRIVNIDRCYYKKTRALAHALYRTGEYKVPDENGVLVSGGLDKLEGMFGFIDQVDKFNNIKKKLNKQPDRYVLTNATLHGFKLKLNAREKAYSKFIYYKFFHGNTCPTIITEGKTDRIYLKAALHSLETSYPELFREKTDSKKKEINLNIFKSNEKTKYFLDLSGGTADLKKFVERYKNNYASYYGSVPKQPVIMVLDNDTGPSDLLNFLRNKVKSCPDDVTEMRKMKYIHVFYNLYIVLTPLSPSGEQTSMEDLFPKDILDIKIDGKKFNKNNDGDSKTEYGKHIFSMRVVRDKKRKIDFKAFCCIFDAIKDIKEHYKLMLNSGSWSHPQFEK

Source

organism	Escherichia coli NCTC 86
ncbi_taxonomy_id	662541
host_organism	Escherichia coli DH5[alpha]

Entity 3 polymer

description	msDNA (67-MER)
formula_weight	20522.1 kDa
src_method	man
entity_count	3

Polymer

type	polydeoxyribonucleotide
strand_id	G,I,H

TCCTTCGCACAGCACACCTGCCGTATAGCTCTGAATCAAGGATTTTAGGGAGGCGATTCCTCCTGCC

Source

organism	Escherichia coli NCTC 86
ncbi_taxonomy_id	662541
host_organism	Escherichia coli DH5[alpha]

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	7

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	617364

fit	/app/data/saxs_computation/s1/9s1f/9s1f.fit
pddf	/app/data/pr_computation/s1/9s1f/9s1f.pr.out
profile	/app/data/saxs_computation/s1/9s1f/9s1f.dat

Cryo-EM structure of activated retron Eco2 (Ec67)

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)