SAXSdb — 9rkv

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1. Structure Basics

entry_id	9rkv
deposition_date	2025-06-14
title	Agrobacterium phage 7-7-1 tail fibers
keywords	Flagella phage, Agrobacterium sp. H13-3, Tail spike, VIRUS; VIRUS
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	75.54 Å
rg_electron	76.91 Å
i0	2564500000.00
molecular_weight	421170.0 kDa
excluded_volume	524610 Å³
envelope_volume	945360 Å³
shell_volume	112310 Å³
envelope_diameter	302.0 Å
shell_rg	62.39 Å
envelope_rg	79.85 Å
shape_rg	76.95 Å
total_rg	76.49 Å
total_atoms	58526
n_residues	4038
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	234.3 Å
rg_real	73.42 Å
rg_real_error	1.86 Å
i0_real	2.5270e+09
i0_real_error	5.8840e+07
rg_reciprocal	72.29 Å
i0_reciprocal	2543000000.0000
total_estimate	0.8542
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	78.1 Å
skewness	0.626
kurtosis	-0.078
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0914
highest_alpha	93950000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.001; Oscil: 0.841; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.452

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Structural protein
formula_weight	14263.9 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	58526

MAIRFHPTNAALVACNAVVDLFDAGGSIEVYTGPQPNDPTVAVSTQTLLVTFAIPAPGYGPAELVPGQNYVRAPGALPAVAVPGASGVAAWARVKNNAGDVIFDGDVGTSASSAFVRLSTTNLTAGVGVSVTASEYRQPTR

Entity 2 polymer

description	Structural protein
formula_weight	31435.2 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	G,H,I,J,K,L

MAGIFFSGGLPCTLTVNAACGIETTGDDCPALYYPPKCNVSVEPLQMNAIISEIANAINAFGDLYDCSRLDNLKAALQKARSICDLPPFADAPDLDDRIAGCFDNTSSTITVQQLVNLVLSQAGGLCDLPQAGGIGDNDLIAGCIGGAEALVSLSTLRGALGGGSISGIIPQEVLFDQWRAGGNWEVSQSTQNRTGFIVRSLKEGIGITVSDLFVATGNGGYQSISQWEATTFLYETDAEGTSIDGGRQQAIAIVFKRGTQWYTKSGDVILPLGSDDGVIRFRTPGYQRLTIWSGAQL

Entity 3 polymer

description	Putative tail fiber
formula_weight	61552.7 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	M,N,O

MVLRPVLVGGLPGCVNLPSNDDCQCWPLWSSDNAYSFGDVVQQGGVLYTANRDIPPGTPFLAGDWTVYTPGATLVPPHREDASYQQYQAVNFNDKLYTARTDLPPGPFDPANWQEISVEGLVEVADSSTIDFSGDGSASDPLTAAVKLDPVAGNLITATPDGLVLLASGIPFPDPSSVNISDNVTLRVDEVTGDDATADGSLQKPYKTIVAAIGASNAGDNIEVYPGSYAGNFAPKSDTTVTGRGFVYVDGNVTIGAAVSGVTVSGLFIDGNLTIAGANGTVEFINTTVSTSIIGTGNNTGWFLFDEVNADSVSITGAGTGEFIFRGGIEQTDFSLNAPSKLLVENRSRVGVVNHLNGLMILKDIGVIVSLTSTAEDNAFTFLAVISSSLFDPDPRTYGALTKTGSCSYAFQDFARSNMAETVTGAKWLVSNGRDIHGNYDPNFYALPNGQSLNSHFEGIDNALQTLQEYSPLGRSVAVDFGFSIIGGWSADETVGVHAVSHETVIPSNMAGSIMVTDSSTLDGVLNVMVGTSVVGTVTITDGAAVFASSEFNLDPGQLVRIVSTSEGTFEYVGLTLVGHRQVVYVD

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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	3.52 Å
resolution_method	—
num_particles	48966

fit	/app/data/saxs_computation/rk/9rkv/9rkv.fit
pddf	/app/data/pr_computation/rk/9rkv/9rkv.pr.out
profile	/app/data/saxs_computation/rk/9rkv/9rkv.dat

Agrobacterium phage 7-7-1 tail fibers

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

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)