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1ddl

DESMODIUM YELLOW MOTTLE TYMOVIRUS

Method: X-RAY DIFFRACTION D_max: 97.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ddl
deposition_date	1999-11-10
title	DESMODIUM YELLOW MOTTLE TYMOVIRUS
keywords	PLANT VIRUS, DYMV, CAPSID PROTEIN, COAT PROTEIN, TYMOVIRUSES, WATER STRUCTURE, RNA, Icosahedral virus, Virus-RNA COMPLEX; Virus/RNA
method	X-RAY DIFFRACTION

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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	30.47 Å
rg_electron	29.78 Å
i0	59846400.00
molecular_weight	61325.0 kDa
excluded_volume	76895 Å³
envelope_volume	100130 Å³
shell_volume	28926 Å³
envelope_diameter	100.2 Å
shell_rg	35.51 Å
envelope_rg	29.96 Å
shape_rg	29.73 Å
total_rg	30.47 Å
total_atoms	4307
n_residues	560
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	97.4 Å
rg_real	30.47 Å
rg_real_error	0.81 Å
i0_real	5.9850e+07
i0_real_error	9.7330e+05
rg_reciprocal	30.48 Å
i0_reciprocal	59850000.0000
total_estimate	0.9027
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.1 Å
skewness	0.214
kurtosis	-0.718
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	8467000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	;RNA (5'-R(PUPUPUPUPUPUP*U)-3') ;
formula_weight	2098.2 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D
atom_count	4670

UUUUUUU

Entity 2 polymer

description	;RNA (5'-R(PUPU)-3') ;
formula_weight	567.4 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	E

Entity 3 polymer

description	DESMODIUM YELLOW MOTTLE VIRUS
formula_weight	20011.7 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C

MEQDKILAHQASLNTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	285

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6. Citations (1)

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length_a	348.546 Å
length_b	348.546 Å
length_c	348.546 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	360

space_group	P 42 3 2
int_tables_number	208
crystal_system	—

resolution	2.700 Å
resolution_low	40.000 Å
r_factor	0.1520
r_work	0.1510
r_free	0.1590

fit	/app/data/saxs_computation/dd/1ddl/1ddl.fit
pddf	/app/data/pr_computation/dd/1ddl/1ddl.pr.out
profile	/app/data/saxs_computation/dd/1ddl/1ddl.dat

DESMODIUM YELLOW MOTTLE TYMOVIRUS

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

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)