SAXSdb — 9x94

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1. Structure Basics

entry_id	9x94
deposition_date	2025-10-20
title	Apo Retron-Eco8 complex
keywords	complex, RNA BINDING PROTEIN/RNA/DNA, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
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	64.60 Å
rg_electron	62.17 Å
i0	7160440000.00
molecular_weight	644350.0 kDa
excluded_volume	776790 Å³
envelope_volume	1275200 Å³
shell_volume	164150 Å³
envelope_diameter	230.1 Å
shell_rg	67.83 Å
envelope_rg	61.40 Å
shape_rg	62.05 Å
total_rg	62.65 Å
total_atoms	86096
n_residues	4818
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	219.0 Å
rg_real	64.40 Å
rg_real_error	2.35 Å
i0_real	7.1600e+09
i0_real_error	1.5010e+08
rg_reciprocal	64.75 Å
i0_reciprocal	7165000000.0000
total_estimate	0.6379
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	82.1 Å
skewness	0.280
kurtosis	-0.339
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	720000000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.972; Smooth: 0.821

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Retron Eco8 reverse transcriptase
formula_weight	43273.2 kDa
ec_number	2.7.7.49
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,E,I,M
atom_count	86096

MKTKKMILVDKVFYEKILSVESFKENIITQSAIPKISNKEVRLISSGSKIFYAINNTSPHSHVQLRLNRFFLSHIPLNSAAKAFVRGGSYLKYLEPHIYGSSYCRLDISSFFNNISFDDVKQSLSPYIKDEYLIGTEQKLIDAILNSVGYESPIRKDKGMIIPMGFRTSPAISNIVFRKMDLLIQDFCAKKGVIYSRYADDMLFSNPRESKLLMSDYFIDEISSLLSIMGFNINQSKYISREKEISINGYVIENKGGNGSIGTIRLSKSKLNTVLKVTHALAQNIPYKNICNKYIKVRLKEKNIKYESKKDEFEKKYYRDQLINYLGGYRSYLISLVKFHSEYKCVNSDFIIQINGILNDIQNHIQKIKKNRRL

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Retron Eco8 OLD nuclease
formula_weight	87373.8 kDa
ec_number	3.1.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,F,J,N

MTIESIRVKNLLSFDDVILRDFRDINCIIGRNNVGKSNLLKVIRYFYAKLENKKVIPLDFHTNYNAVGEITFTFDTTRIKKIVTSRKNNGRFHKHIYNTLFKSSSVKLNFEELIARKNSTNKSFFSLTLTICKDDSVMWSVDDPKVRSLLATLYPFLYIETRHIDLYDWNPIWKLISNLNSFNFDDVDHDELVNFLDEKISSRKGDYKKYIDRVVSVIDTKPYTYKEKVINYIKVAIKGDSFVNAGEELFTQSDGTNSNKFLETLLHLLITLTRTEFISPIVYIDEPEVGLHPKLAESFVSNLNKIYSKFKKTSELSGPGRYKTPYPNIFYSTHSPSILKQTIKLFGKDQQVLHFSKKKDGSTRVNKINSTYSDERFLNIFSDNEARLFFSEYIVFVEGATELELFRNLSLLNLYPAFSLADIYDANEVILANINPGYSKASIPFVIIKDIDTLIDYSIKTEKFSLRPLFEKMIKELTKEFDYYDTGFGRVRKEIDLFSDIQSSTKKHMDSGLFFKRFSLHNLSSRINKVSRKLNRYFMTTTIEGALINEQSLPYFFNWIGDVILTQMTINNPNPDKFIEAMRRRYNIKSQVVPLFKSVFCIGLNHPVYSSAVDKQALRIKLSFLNYLKRKVYSDFNNEKEIVLALRLAFGGKTETQYTLDKLRKDGEAELFREKIKNYKNNELFFLEPQMTKTSGWVTTFLNYTIEKITSEESDDDRIRQKLSFIFPEIISIIEQASSSIEAEESSLTG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	RNA (81-MER)
formula_weight	25986.4 kDa
src_method	man
entity_count	4

Polymer

type	polyribonucleotide
strand_id	C,G,K,O

AAGCUUCUUCUUCGAUAGAAGCUGAGGAGUCCAGUUUGACUGGAUAAGGUGUUCGCCAUCUCUAGCCUCAGUAAAAACUAG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	DNA (75-MER)
formula_weight	23126.8 kDa
src_method	man
entity_count	4

Polymer

type	polydeoxyribonucleotide
strand_id	D,H,L,P

CAAGACCAATCTTTACACTCTGTGAGTATTAAAGTTACCTATAGCGCCAAGTGCGCAAAGGATGAGCTAGTTTTT

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

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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	2.570 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.57 Å
resolution_method	—
num_particles	303229

fit	/app/data/saxs_computation/x9/9x94/9x94.fit
pddf	/app/data/pr_computation/x9/9x94/9x94.pr.out
profile	/app/data/saxs_computation/x9/9x94/9x94.dat

Apo Retron-Eco8 complex

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 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)