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9ums

Cryo-EM structure of bacteriophage P1 connector

Method: ELECTRON MICROSCOPY D_max: 201.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ums
deposition_date	2025-04-22
title	Cryo-EM structure of bacteriophage P1 connector
keywords	connector, phage, VIRAL PROTEIN; VIRAL 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	58.13 Å
rg_electron	59.20 Å
i0	377118000.00
molecular_weight	162030.0 kDa
excluded_volume	203040 Å³
envelope_volume	336310 Å³
shell_volume	51532 Å³
envelope_diameter	223.3 Å
shell_rg	52.70 Å
envelope_rg	59.49 Å
shape_rg	59.28 Å
total_rg	58.72 Å
total_atoms	11411
n_residues	1448
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	201.9 Å
rg_real	59.11 Å
rg_real_error	2.31 Å
i0_real	3.7710e+08
i0_real_error	8.1870e+06
rg_reciprocal	57.24 Å
i0_reciprocal	376000000.0000
total_estimate	0.6843
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	37.4 Å
skewness	0.590
kurtosis	-0.431
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0002
highest_alpha	29130000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.456; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.278; Smooth: 0.246

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Gp7
formula_weight	27165.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	11411

MAGFFDDMFEDTEPSQQVTGDNLPDTESDPDIPGEGSELIEEEDIDAEIETDGVNVGNIVDPVEDNHLPNLDHGLLSDSGVRHRYQGHAVFNNLVRMDWLKAIKLDPDSFDAVLYRAIPYRNKNAPETAPEIIEPNQRIYDYQDPELITALDCPDEMDAFYALYDGSDNTGISDSALILRLAAVNVPVGSMLEWLEQLSDGTTIRRFWYIHKIFNYGTARVGSLFYCVPSRAFEGNFIGDSE

Entity 2 polymer

description	Prt
formula_weight	62813.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MADNKITLSSVRKALAGVFKDNGERDNILLSALAVHGGSGYLFSRAGAPVQLSGFLGGKPGDSGMAGDGLVDGSRFIFDEVQLPEDRLQRYPLLEEMAVYSTIATALNIHITHALSFDKKTGQTFSIVPVHNGNDSDYDAAQALCGELMNDIGRTINKEVAGWAFIMSVFGVAYVRPYAKEGIGITSFECSYYTLPSFIKEFEVSGNLAGFSGDYLKDASGKMVFADPWAIIPMKIPYWRPKSNLMPVHTGHKAYSLLDNPEERTPIETQNYGTSLLEYAYEPYMNLRSAIRSLKATRFNASKIDRIIGLAMNSLDPVKAADYSRTITQTLKRAADLMERRARGANNMPTVTNTLLPIMGDGKGQMTIDTQTIQADINGIEDILTYMRQLAAALGLDYTLLGWADQMSGGLGEGGFLRTAIQAAMRASWIQQGVEEFIQRAIDIHLAFKYGKVYPEGDRPYKIEFHSVNTALQQEHNDNRDSQANYATIVTQILDAVSNNSVLANSDAFKRYLFSDVLEIDEKISEALVNELKAKSEDDDHLMDSIIKTPPQELAQILESVFKEGNDND

Entity 3 polymer

description	PmgC
formula_weight	21041.0 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E

MTPRQLLEDVKTRFTPLIADEPALLESLLRKALGTYQDRAGHIKRIRFTDQASNSLACPADFLALVSVTDHTGDLVYSDVYDGNIELEDTHRAVYPLNVSYLANLRDMDLDNGEVPPEIIGLLSDYLEVLIAIPNTDRLRRISIAGKLDASNLSDENTLYQRKLDLEEKMSATRAIIPGIVLFSSMLK

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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	3.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.50 Å
resolution_method	—
num_particles	32542

fit	/app/data/saxs_computation/um/9ums/9ums.fit
pddf	/app/data/pr_computation/um/9ums/9ums.pr.out
profile	/app/data/saxs_computation/um/9ums/9ums.dat

Cryo-EM structure of bacteriophage P1 connector

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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)