SAXSdb — 9xps

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1. Structure Basics

entry_id	9xps
deposition_date	2025-11-17
title	The neck structure of the Phage Phikz
keywords	neck, 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	70.66 Å
rg_electron	70.39 Å
i0	3935010000.00
molecular_weight	536050.0 kDa
excluded_volume	672060 Å³
envelope_volume	1248400 Å³
shell_volume	145860 Å³
envelope_diameter	233.9 Å
shell_rg	74.97 Å
envelope_rg	67.42 Å
shape_rg	70.38 Å
total_rg	70.48 Å
total_atoms	37802
n_residues	4640
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	271.9 Å
rg_real	75.02 Å
rg_real_error	2.25 Å
i0_real	3.9760e+09
i0_real_error	8.0140e+07
rg_reciprocal	70.97 Å
i0_reciprocal	3938000000.0000
total_estimate	0.8856
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	86.5 Å
skewness	0.555
kurtosis	0.347
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.7768
highest_alpha	242900000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 0.845; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.876

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	PHIKZ099
formula_weight	54814.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	37802

MALLTIEDEELPVNPEVKPVNPKECPDVFRGIAVDTKYVPRSDLMAWITGSNWRVDYFSQILREDQEPTALDIHRRPDKQQYIAIKGMDLKVTQALQYNQAENTTKFKVDGTGFTYPFLVPQKNDMFIADVGDGRSGLFTITSVRRQTILRDSTYAVTWKMIHYVTQQEYDDLITKSQMSYYYSSTSLMNGCGPFVTEQEQEDNTNLTKLYKEIIRNYITEFYSPQHQTFLVPDQLTKTYDHFAVKAFLQMVDASADPRMYKIKLLNVFSEPVMSQPTVWDAIVRQDVARMCYATEKAHLVTTKISRWKPVFQAIGFTGIARMVFPIDAPIDVESRYDGETMCRPDGQPFREGRPMREAPGPYRTQAERNLPWFKRIDPQYEDRVKPWQIPADIYPIVRDNYYVFTEAFYRGDKKLMSKLELCVWAMINGEAVNADQLREVAKCSRSWDNLERYYYHIVLLSLIKYSLR

Entity 2 polymer

description	PHIKZ029
formula_weight	77712.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	x

MAYYNAVPRVVFNGIRDRSRRPLIRPDITFAQHCPLLRLFTETGPTETTYVGDSDDGFASIYGQASLDPRSKFFNTQSLLALNLLGRGNGFYVKRLRPEDAANPSRLIVAIEIVEDEIPLTIRRLSGFNYPNSVRDIGNAPVPTTDKVDGLKARIILIEDNTSEVGTQRVLPGTLVSDKDGSQSLVYPLFEAPVSFFGKLGDSNGMRVWSTTTADIEEFDEAAMAKFKTRQFRIQLIEKPEVGTSPVIVKTADQQDYLNITFDKGVYSDMYNADLYVGDVLVDSYSDDGVVSGLSPLYSPFSQFYVYHENIDLVRQMIYDTEMRVNPAAAAHTTAPGEIDFLTFLAVDGDPYQGIQVLGPLDGGITLGKDGNIYASGGTDGTTDLEEYAKLVDIENINFGKLNDRYNNIAEYQFGVLYDTGLPMESKYRAMRVLSARRDLQYFFTTFVETDSRLPDEATELSRVQQIITRLKAFPESTLYGTGVCRAMIVMQSGKLMDGTYRKYVPQLLDVAMSWARYAGAGTGNLVPGMEMDVSPNNRVTFVKDLNVKFFDDRVRAQAWANGATWSQSYDHRSSYYPCLRSVMLDDTSVLLSPITVNICCVLIRLIHKVHAQFSGNATLTPEQLVERCDEYILDLVRDMFGTRVNIIPRTEITPIDANNGTSWTCNVTVEANNPRTTLNFNLETVRIETPPAQQ

Entity 3 polymer

description	PHIKZ030
formula_weight	32686.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	y,z

MARYNDPMAPETGYGAGGARNTVNLAQAGTNVFRPDLANLATNTPYVARNLVPFLLDAPRFFKYASNTNWLVACLKAFVETHTRTIDGLQRTLTVDNAEAPWGGSGEVIQTATNVTRARSNPNFGCWELQNRAIQRFLQWWINYGIADENTKVPRIVSDGIVPVEKYDATFYGMTVLFVEPDPTFQDCVNAYLCTNMFPLTTGPWENRKDASQIGQNLDLNVEFSALTDVSEGVQEYARQMFRKLNIRGMNPNNQKLDWGGLSADVLRARNGIQDQIERAVGNRVTYDGVGLS

Entity 4 polymer

description	PHIKZ098
formula_weight	63225.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	w

MPNTTLVLPDVYESVTRRVAADIIGQLAKMMGLPEDTLVQFPGNVQTVPMNGGMFGNCCDSANVVKFDPEDHIIITYDEVADERYTLSTDVKNHQNFPWFVDETRGVRITPVRRFVDVRFDIEYKSKNITLAQRWLDEQRLWFSNNGQELVHTLTYHVDVPMPVQGILAAIYNTAQNSHWPMEETFPEYLNKYFTFPTTELADLSQKNKSLVIYERQVDVIGWYDYTSTPPTPEYDSESDGSYNVRFSYFLTYARPTHVWIEYPLTVHQCLVPSVIRPKYIYENYQQVDRKVSQFRGSLYHKFLLIRDKKIPYIQHPDIDTWDTDNIPINQLTFFSGLLTLCPDEIESGTLMSFDQLGRYSFSPFFLEYFEGVGTKAIDQNGIFQVRLYENDNYTRAECYLDGLMLKTKWKLDPCKVYHVQISIHKNLLLVFDDRWRCLQRYPRVCWTIFNLFGVGIGRKPFEEVKLLGKGRDRLPSEECPGEGTTCHTQCLNPTTEGVINWKDIVDAREEMNTRIGPDWDPTYLMGPLTVLYGNIITERKE

Entity 5 polymer

description	PHIKZ034
formula_weight	29899.9 kDa
src_method	nat
entity_count	8

Polymer

type	polypeptide(L)
strand_id	1,3,5,6,4,7,8,2

MSCCKAPVKPDTSIDIDHLGGGCQTYNHLQDMFFYLKEERLNAKPCDLSRYSIQYSYVDSMTYLYVLTDELTGETISWSVTKEFEKESPQAAFERDYIERELIYNRGIKRALDDMLEGLADADPSNVYKLERTDYGYRILRRINDELGAVIFKLSYTIHRGPIITPFSDKCTVPENVPDIFPTETQRALSRLVYRFHKLGVIFGDWVPDHVQKYNKMELTGYTRRTMDSYVILNMAIQSINLTDPELVTYHKYYSI

Entity 6 polymer

description	Endolysin gp144
formula_weight	28850.0 kDa
ec_number	4.2.2.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

MKVLRKGDRGDEVCQLQTLLNLCGYDVGKPDGIFGNNTFNQVVKFQKDNCLDSDGIVGKNTWAELFSKYSPPIPYKTIPMPTANKSRAAATPVMNAVENATGVRSQLLLTFASIESAFDYEIKAKTSSATGWFQFLTGTWKTMIENYGMKYGVLTDPTGALRKDPRISALMGAELIKENMNILRPVLKREPTDTDLYLAHFFGPGAARRFLTTGQNELAATHFPKEAQANPSIFYNKDGSPKTIQEVYNLMDGKVAAHRK

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6. Citations (1)

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resolution	3.520 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.52 Å
resolution_method	—
num_particles	35244

fit	/app/data/saxs_computation/xp/9xps/9xps.fit
pddf	/app/data/pr_computation/xp/9xps/9xps.pr.out
profile	/app/data/saxs_computation/xp/9xps/9xps.dat

The neck structure of the Phage Phikz

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)