Cryo-EM structure of GroEL-ADP

Method: ELECTRON MICROSCOPY D_max: 171.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ynj
deposition_date	2025-10-10
title	Cryo-EM structure of GroEL-ADP
keywords	protein folding, molecular chaperone, tetradecamer, CHAPERONE; CHAPERONE
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	64.74 Å
rg_electron	63.67 Å
i0	8662310000.00
molecular_weight	778700.0 kDa
excluded_volume	973500 Å³
envelope_volume	1575300 Å³
shell_volume	196050 Å³
envelope_diameter	189.0 Å
shell_rg	75.47 Å
envelope_rg	59.83 Å
shape_rg	63.69 Å
total_rg	63.75 Å
total_atoms	54418
n_residues	7350
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	171.5 Å
rg_real	64.00 Å
rg_real_error	0.61 Å
i0_real	8.6620e+09
i0_real_error	1.4110e+08
rg_reciprocal	65.35 Å
i0_reciprocal	8682000000.0000
total_estimate	0.8380
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	92.9 Å
skewness	-0.102
kurtosis	-0.538
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	4072000000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (2)

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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	4.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.20 Å
resolution_method	—
num_particles	78179

description	Chaperonin GroEL
formula_weight	55349.3 kDa
ec_number	5.6.1.7
src_method	man
entity_count	14

Cryo-EM structure of GroEL-ADP

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 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
atom_count	54418

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	14

fit	/app/data/saxs_computation/yn/9ynj/9ynj.fit
pddf	/app/data/pr_computation/yn/9ynj/9ynj.pr.out
profile	/app/data/saxs_computation/yn/9ynj/9ynj.dat