RNA Vault waist region, focused refinement (MVP/TEP1 sample)

Method: ELECTRON MICROSCOPY D_max: 165.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11dv
deposition_date	2026-02-18
title	RNA Vault waist region, focused refinement (MVP/TEP1 sample)
keywords	RNA Vault, ADPR, ADP-ribose, Major Vault Protein, STRUCTURAL PROTEIN; STRUCTURAL 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	48.09 Å
rg_electron	48.35 Å
i0	238895000.00
molecular_weight	129010.0 kDa
excluded_volume	162430 Å³
envelope_volume	235360 Å³
shell_volume	43760 Å³
envelope_diameter	165.9 Å
shell_rg	46.75 Å
envelope_rg	47.71 Å
shape_rg	48.33 Å
total_rg	48.32 Å
total_atoms	18258
n_residues	1125
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	165.8 Å
rg_real	48.51 Å
rg_real_error	1.89 Å
i0_real	2.3890e+08
i0_real_error	5.0180e+06
rg_reciprocal	48.09 Å
i0_reciprocal	238800000.0000
total_estimate	0.8544
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.2 Å
skewness	0.416
kurtosis	-0.471
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	11580000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.877; Smooth: 0.605

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Major vault protein
formula_weight	99452.8 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	18618

MATEEFIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPMRMVTVPPRHYCTVANPVSRDAQGLVLFDVTGQVRLRHADLEIRLAQDPFPLYPGEVLEKDITPLQVVLPNTALHLKALLDFEDKDGDKVVAGDEWLFEGPGTYIPRKEVEVVEIIQATIIRQNQALRLRARKECWDRDGKERVTGEEWLVTTVGAYLPAVFEEVLDLVDAVILTEKTALHLRARRNFRDFRGVSRRTGEEWLVTVQDTEAHVPDVHEEVLGVVPITTLGPHNYCVILDPVGPDGKNQLGQKRVVKGEKSFFLQPGEQLEQGIQDVYVLSEQQGLLLRALQPLEEGEDEEKVSHQAGDHWLIRGPLEYVPSAKVEVVEERQAIPLDENEGIYVQDVKTGKVRAVIGSTYMLTQDEVLWEKELPPGVEELLNKGQDPLADRGEKDTAKSLQPLAPRNKTRVVSYRVPHNAAVQVYDYREKRARVVFGPELVSLGPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVITIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASRVRGAVASVTFDDFHKNSARIIRTAVFGFETSEAKGPDGMALPRPRDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEALSMAVESTGTAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELQRVQKVRELELVYARAQLELEVSKAQQLAEVEVKKFKQMTEAIGPSTIRDLAVAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTAFGLLGMGPEGQPLGRRVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	360

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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	triclinic

resolution	2.33 Å
resolution_method	—
num_particles	1016071

fit	/app/data/saxs_computation/1d/11dv/11dv.fit
pddf	/app/data/pr_computation/1d/11dv/11dv.pr.out
profile	/app/data/saxs_computation/1d/11dv/11dv.dat