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9vzi

Cyanopodophage Pan3 Needle

Method: X-RAY DIFFRACTION D_max: 71.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vzi
deposition_date	2025-07-22
title	Cyanopodophage Pan3 Needle
keywords	Cyanophage, Virus, Needle; VIRUS
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	24.29 Å
rg_electron	23.15 Å
i0	27975700.00
molecular_weight	37349.0 kDa
excluded_volume	45275 Å³
envelope_volume	54775 Å³
shell_volume	20568 Å³
envelope_diameter	75.0 Å
shell_rg	29.16 Å
envelope_rg	23.02 Å
shape_rg	23.10 Å
total_rg	23.97 Å
total_atoms	2587
n_residues	357
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	71.6 Å
rg_real	24.24 Å
rg_real_error	0.38 Å
i0_real	2.7980e+07
i0_real_error	3.2300e+05
rg_reciprocal	24.26 Å
i0_reciprocal	27980000.0000
total_estimate	0.9163
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.7 Å
skewness	0.180
kurtosis	-0.654
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	3238000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.996; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.934

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Needle protein
formula_weight	20252.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,D
atom_count	2778

MSLRLDRLQRGVPIVDGQGRPNTQYQNLWQRTVKALEADSAATADILQELADQLALIVAAQAAADAAQATADAALGAAGNPVLTELITGQNATSNVLRFTLENGASRQFTAQVRAGPLTGNCTQTIQLESRVAGGTYANLGTAGVDSGTTGDTLFPDTLGTVSNSSGQTQVYEVRCVTSTTGPGTGAIDQPVSYVTG

Source

organism	Pseudanabaena phage Pan3
ncbi_taxonomy_id	2981586
host_organism	Escherichia coli

Entity 2 non-polymer

description	IODIDE ION
formula_weight	126.9 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	191

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6. Citations (1)

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length_a	71.403 Å
length_b	71.403 Å
length_c	172.706 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 41 2 2
int_tables_number	91
crystal_system	—

resolution	2.600 Å
resolution_low	13.020 Å
r_factor	0.1828
r_work	0.1809
r_free	0.2199

fit	/app/data/saxs_computation/vz/9vzi/9vzi.fit
pddf	/app/data/pr_computation/vz/9vzi/9vzi.pr.out
profile	/app/data/saxs_computation/vz/9vzi/9vzi.dat

Cyanopodophage Pan3 Needle

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