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9y9c

Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.

Method: ELECTRON MICROSCOPY D_max: 239.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y9c
deposition_date	2025-09-14
title	Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.
keywords	Phage-bacterial defense complex, Abortive infection Ring-Activated Zinc-Finger RNase (RAZR), 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	98.05 Å
rg_electron	97.78 Å
i0	9368790000.00
molecular_weight	811360.0 kDa
excluded_volume	1008600 Å³
envelope_volume	1981200 Å³
shell_volume	160400 Å³
envelope_diameter	283.3 Å
shell_rg	105.10 Å
envelope_rg	95.21 Å
shape_rg	97.71 Å
total_rg	98.09 Å
total_atoms	112779
n_residues	7248
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	239.9 Å
rg_real	94.36 Å
rg_real_error	0.73 Å
i0_real	9.0210e+09
i0_real_error	1.5840e+08
rg_reciprocal	97.17 Å
i0_reciprocal	9337000000.0000
total_estimate	0.9060
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	149.9 Å
skewness	-0.023
kurtosis	-0.924
angular_range	— – 0.0800 Å⁻¹
current_alpha	0.3823
highest_alpha	221900000.0000
n_real_points	17
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.999; Stabil: 0.970; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Gp77
formula_weight	25475.7 kDa
src_method	man
entity_count	24

Polymer

type	polypeptide(L)
strand_id	IA,IB,IC,ID,IE,IF,IG,IH,II,IJ,IK,IL,IM,IN,IO,IP,IQ,IR,IS,IT,IU,IV,IW,IX
atom_count	112779

MKLSDQFDKVLPALHKARSLFVKVKKDRQNSHLKNRYATLDSVLDAITPALMDNELMIMQDGERIDVSTLRVETTVMHVSGQWVKFYFDIPIVKNDPQGVGSAFTYGRRYSAAAAFGLSQADDDAQIAVKTVNDWKRDIEKCESVGELQEVLKNAWKSSDAASKQVIRDHYEKRKAEIEIGGARGFNPAKPKENLASDAVDTPNSEKVKSQSITDFEGSSGHHHHHH

Source

organism	Escherichia phage SECphi27
ncbi_taxonomy_id	2496550
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	DUF4145 domain-containing protein
formula_weight	24707.0 kDa
src_method	man
entity_count	24

Polymer

type	polypeptide(L)
strand_id	OA,OB,OC,OD,OE,OF,OG,OH,OI,OJ,OK,OL,OM,ON,OO,OP,OQ,OR,OS,OT,OU,OV,OW,OX

MAEYYPAVFEAEAFNCPHCGVYARQFWRRMYGSARELAQRTTEFRMSTCSHCGDDAYWYDGNMIIPAAGNVELPNPDMPDNCKSDYMEARSIINLSPKGAAALLRLCLQKLMVHLGEPGENINKDIRSLVQKGLPVRIQQAADICRIVGNQAVHPGEISLDDDPQLAHGLFKLLNIIVDDRITRPKEIEAMFQSMPEGPRQGIENQDRQAREQQQAANE

Source

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

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	24

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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	3.50 Å
resolution_method	—
num_particles	28191

fit	/app/data/saxs_computation/y9/9y9c/9y9c.fit
pddf	/app/data/pr_computation/y9/9y9c/9y9c.pr.out
profile	/app/data/saxs_computation/y9/9y9c/9y9c.dat

Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.

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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)