← Back to search

9vz0

Cryo-EM structure of the head of contracted P1

Method: ELECTRON MICROSCOPY D_max: 152.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9vz0
deposition_date	2025-07-21
title	Cryo-EM structure of the head of contracted P1
keywords	head, contracted phage P1, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	46.92 Å
rg_electron	48.51 Å
i0	17426500.00
molecular_weight	31399.0 kDa
excluded_volume	38736 Å³
envelope_volume	68511 Å³
shell_volume	15302 Å³
envelope_diameter	158.1 Å
shell_rg	38.06 Å
envelope_rg	48.07 Å
shape_rg	48.51 Å
total_rg	47.80 Å
total_atoms	2203
n_residues	287
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	152.3 Å
rg_real	48.41 Å
rg_real_error	2.05 Å
i0_real	1.7430e+07
i0_real_error	3.1380e+05
rg_reciprocal	46.94 Å
i0_reciprocal	17390000.0000
total_estimate	0.5648
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.4 Å
skewness	0.560
kurtosis	-0.798
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	692800.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.109; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.017; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Hdf
formula_weight	22189.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	2203

MCQMTKNKYATVDFDQVNEKGLKSLITAINKTGVTVIEVDSSNRATTKDGVKVKTAKLVLSDGQILAIQVNDTGDISSVKLNGKAIPNAQSPDIKTLGTVMGQAARKNSAKFQKSLIAKAKRVANPVDKKPAVKSNFQRLQEAKQRNAQVVAAYKSAQNSVSFNQQQITDLRAKLDKETGRLNNEKARNGELKRRLKQLKAGN

Entity 2 polymer

description	Defense against restriction protein A
formula_weight	69550.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MEQFNINKGMTIKPGLDVLPPPVTDDEYRALMAGEDRYLMTESNTLEEIEATFFYDTPIHWCATDLLEAISSTRLQLHRTMQAFVRALNQKLNGTGISAGSDKTGDVAQSGARAIGGAEIGRARNVNGLPVLPAIIPLSDGQTISILFHSPTAENRITNSDTLVAFQFLLNKKDVTHTVAPMSGRDMTLAQVTMKLANLAEKNSAKFQRAQKKKKALVDEITQLQADSDQKEDAMSDLADQVAAVEGQKADLEQKINAVASEADSLYEENERLQGEIDRLNRTGGRDTIAPAGMTGGHSRALTDRLASIKNRMHMDGEATLSNGASMKQFIGDGEGYIQLTDPDGSVYMIKAKSIQGVDMADAIGKLFKAYKAGNVSEYLVQPEEHKPENVEPESAEDTGSSSPEPEVSVGAYRYALQMRPAAPGAIPEGNKAILPRPDEGDPYYEYARYGIATYDTPLSDQQMSEYDLKLLPREDSFDFLAKTLTNGPFGKYAQKALELATNSPDEFRVMLKTQFQKTFPNIAFPGGAGTEKMVQSMINALQAEVGEITQPEPAPAQPDETVSEADAEANKAIEYLNNVMDMQSTDMAEIRNARGNVREAIAALQTAGRFEENEELVNGAARHLADLLVAIQKAGVAA

▶

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	—

resolution	4.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.00 Å
resolution_method	—
num_particles	3200

fit	/app/data/saxs_computation/vz/9vz0/9vz0.fit
pddf	/app/data/pr_computation/vz/9vz0/9vz0.pr.out
profile	/app/data/saxs_computation/vz/9vz0/9vz0.dat

Cryo-EM structure of the head of contracted P1

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)