SAXSdb — 9ukm

▼

1. Structure Basics

entry_id	9ukm
deposition_date	2025-04-18
title	Cryo-EM structure of bacteriophage P1 head
keywords	head, phage, 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	80.76 Å
rg_electron	82.35 Å
i0	2011290000.00
molecular_weight	380490.0 kDa
excluded_volume	476890 Å³
envelope_volume	893250 Å³
shell_volume	99160 Å³
envelope_diameter	324.4 Å
shell_rg	66.27 Å
envelope_rg	89.04 Å
shape_rg	82.23 Å
total_rg	82.47 Å
total_atoms	26773
n_residues	3452
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	224.0 Å
rg_real	73.24 Å
rg_real_error	1.60 Å
i0_real	1.9310e+09
i0_real_error	4.5580e+07
rg_reciprocal	74.69 Å
i0_reciprocal	1979000000.0000
total_estimate	0.9021
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	82.5 Å
skewness	0.537
kurtosis	-0.314
angular_range	— – 0.0950 Å⁻¹
current_alpha	0.0526
highest_alpha	72900000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.001; Oscil: 0.903; Stabil: 0.975; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.188

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Gp23
formula_weight	62326.4 kDa
src_method	nat
entity_count	7

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G
atom_count	26773

MSNLREYQNRIADIAKRSKAVLGWASTAQFGTDNQFIKDDAARAASILEAARKDPVFAGISDNATAQIATAWASALADYAAAHKSMPRPEILASCHQTLENCLIESTRNSMDATNKAMLESVAAEMMSVSDGVMRLPLFLAMILPVQLGAATADACTFIPVTRDQSDIYEVFNVAGSSFGSYAAGDVLDMQSVGVYSQLRRRYVLVASSDGTSKTATFKMEDFEGQNVPIRKGRTNIYVNRIKSVVDNGSGSLLHSFTNAAGEQITVTCSLNYNIGQIALSFSKAPDKGTEIAIETEINIEAAPELIPLINHEMKKYTLFPSQFVIAAEHTVQAAYEAQREFGLDLGSLQFRTLKEYLSHEQDMLRLRIMIWRTLATDTFDIALPVNQSFDVWATIIRGKFQTVYRDIIERVKSSGAMGMFAGADAASFFKQLPKDFFQPAEDYIQTPYVHYIGTLFGNVKVYEVPAGICKNLTTENIQFSSMDVLCYVRDENPGKAGFVTGDAVPAIPFQHPTTPALVNRTTLWGSAINDMHPRNGADYFTRVTLTMAKKGGLNFISGDTIDAGDSE

Entity 2 polymer

description	Hdf
formula_weight	22189.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MCQMTKNKYATVDFDQVNEKGLKSLITAINKTGVTVIEVDSSNRATTKDGVKVKTAKLVLSDGQILAIQVNDTGDISSVKLNGKAIPNAQSPDIKTLGTVMGQAARKNSAKFQKSLIAKAKRVANPVDKKPAVKSNFQRLQEAKQRNAQVVAAYKSAQNSVSFNQQQITDLRAKLDKETGRLNNEKARNGELKRRLKQLKAGN

Entity 3 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	3.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.60 Å
resolution_method	—
num_particles	11800

fit	/app/data/saxs_computation/uk/9ukm/9ukm.fit
pddf	/app/data/pr_computation/uk/9ukm/9ukm.pr.out
profile	/app/data/saxs_computation/uk/9ukm/9ukm.dat

Cryo-EM structure of bacteriophage P1 head

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)