SAXSdb — 11eq

▼

1. Structure Basics

entry_id	11eq
deposition_date	2026-02-19
title	RNA Vault with BAD bound (MVP/TEP1 sample)
keywords	RNA Vault, BAD, benzamide adenine dinucleotide, Major Vault Protein, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	— Å
rg_electron	223.10 Å
i0	621317000000.00
molecular_weight	6751800.0 kDa
excluded_volume	8454200 Å³
envelope_volume	46024000 Å³
shell_volume	1841600 Å³
envelope_diameter	670.8 Å
shell_rg	223.30 Å
envelope_rg	183.90 Å
shape_rg	223.00 Å
total_rg	223.50 Å
total_atoms	954252
n_residues	59592
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

▼

3. P(r) Analysis (GNOM)

dmax	530.3 Å
rg_real	212.40 Å
rg_real_error	1.08 Å
i0_real	5.4930e+11
i0_real_error	1.3690e+10
rg_reciprocal	172.10 Å
i0_reciprocal	336400000000.0000
total_estimate	0.8875
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	303.0 Å
skewness	-0.308
kurtosis	-0.707
angular_range	— – 0.0350 Å⁻¹
current_alpha	3.4630
highest_alpha	50850000000.0000
n_real_points	8
gnom_version	4.1.3
quality_criteria	AN1: 1.439; Oscil: 0.992; Stabil: 0.912; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Major vault protein
formula_weight	99452.8 kDa
src_method	man
entity_count	78

Polymer

type	polypeptide(L)
strand_id	;A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8,9,0,AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL,AM,AN,AO,AP ;
atom_count	954252

MATEEFIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPMRMVTVPPRHYCTVANPVSRDAQGLVLFDVTGQVRLRHADLEIRLAQDPFPLYPGEVLEKDITPLQVVLPNTALHLKALLDFEDKDGDKVVAGDEWLFEGPGTYIPRKEVEVVEIIQATIIRQNQALRLRARKECWDRDGKERVTGEEWLVTTVGAYLPAVFEEVLDLVDAVILTEKTALHLRARRNFRDFRGVSRRTGEEWLVTVQDTEAHVPDVHEEVLGVVPITTLGPHNYCVILDPVGPDGKNQLGQKRVVKGEKSFFLQPGEQLEQGIQDVYVLSEQQGLLLRALQPLEEGEDEEKVSHQAGDHWLIRGPLEYVPSAKVEVVEERQAIPLDENEGIYVQDVKTGKVRAVIGSTYMLTQDEVLWEKELPPGVEELLNKGQDPLADRGEKDTAKSLQPLAPRNKTRVVSYRVPHNAAVQVYDYREKRARVVFGPELVSLGPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVITIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASRVRGAVASVTFDDFHKNSARIIRTAVFGFETSEAKGPDGMALPRPRDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEALSMAVESTGTAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELQRVQKVRELELVYARAQLELEVSKAQQLAEVEVKKFKQMTEAIGPSTIRDLAVAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTAFGLLGMGPEGQPLGRRVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) ;
formula_weight	662.4 kDa
src_method	syn
entity_count	78

▶

6. Citations (1)

▶

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	triclinic

resolution	2.17 Å
resolution_method	—
num_particles	20744

fit	/app/data/saxs_computation/1e/11eq/11eq.fit
pddf	/app/data/pr_computation/1e/11eq/11eq.pr.out
profile	/app/data/saxs_computation/1e/11eq/11eq.dat

RNA Vault with BAD bound (MVP/TEP1 sample)

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)