SAXSdb — 9yft

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1. Structure Basics

entry_id	9yft
deposition_date	2025-09-26
title	N4 Bacteriophage Asymmetric Tail Gating Complex
keywords	bacteriophage, 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	49.70 Å
rg_electron	51.32 Å
i0	599545000.00
molecular_weight	200940.0 kDa
excluded_volume	251160 Å³
envelope_volume	362150 Å³
shell_volume	66613 Å³
envelope_diameter	230.0 Å
shell_rg	47.71 Å
envelope_rg	54.49 Å
shape_rg	51.31 Å
total_rg	51.21 Å
total_atoms	14173
n_residues	1832
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	133.1 Å
rg_real	44.28 Å
rg_real_error	0.50 Å
i0_real	5.6800e+08
i0_real_error	8.2500e+06
rg_reciprocal	49.71 Å
i0_reciprocal	597800000.0000
total_estimate	0.7231
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	49.9 Å
skewness	0.482
kurtosis	-0.196
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.1040
highest_alpha	60650000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.010; Oscil: 0.898; Stabil: 0.989; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.784

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Gp53
formula_weight	97954.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	FA
atom_count	14173

MGLFSSKTKIYVASSVYNLAGDIHKRPNYLKTTVIGNIVSKSDFSMGDTITDSYLNGPGIRLRRFPGWAATNYDPSIGIAYGNLSILSQVDPEVVKWQVPQKAGYEVQVQSSRIGFGDFEEWADKFLYENYPDRITEEFEIDIMDDDRIVLTATDGSELSFYPKNYSQDAMYLYVNYYYIQPTSVADPVVHPAVSVSSADDLPSTSEWTQVSQNHTPKSATLKTVTHIKSVFSDGRPDEESTNTEEEQVSWTNFSDVYEKEFREPSEVGLIIIRKTIMTQVQTGTVSTGSTTNTEVIDLGGGVTETRTTTVTTDTLGHTWSYQNTDVVTTLSAGGMPQLFIYKQNSGNAVLDALFINKTTNNRFYSFIPIRSDKNWISGSTYTLCKKAFKKATGGKISDIMDDLKKNKDIGDIQYIYAVFGCSLNSPENTAKEYIYRFFQLVNQSMPADPNYPTMDALVEGFAQANRDFDAYQEWWESRSGNRDIPIGKPPKRPVYPTIPSKSINIRSNGGYRYNMTISWNFIEESVGSGKAFSGAKKGQLKFAYEGTVVLMQKAVMYSEKGNDKVGFTIYRLDKITMYWQDGDNSWRKISVYGLNHNNNVYKNKSVSISGVDALNDDEESGFIIPLHNNIYRSMSLVNGTQLSTACCYLVLNSYKKVKKKWYQSGIFKVVVVVVAVVVSVFFTPAAGAGVMGTAASIGAALGFAGLAAIIVGAVANAIAAMILMSIIQTVSVSLLGDKIGIIVATIASMVAMNVGTALSTGSSMSTMLGEMMKADNIIKLTSSVGNGISDYINASAMETVKKTEKLMAEYRDQMKTIQEKYEEMFGTEGMGYIDPMNLTNVGQQFEPLDSFLSRTLMTGHDIADMSNNMITNFTDITLQLDLDT

Entity 2 polymer

description	Non-contractile tail sheath
formula_weight	154255.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	LA

MSIEDYLKGKNCLASPNYDPDDQHSSWREDLPQFKKDREHLTLVNTRRNRTYNTKLNRFDPEYWVVDYNALMVATIIPYGSKSFKVPCQWRTNKDFLGVRWMTEDTFDHHLYRYETDPNYLGLILAFRHNPDEPDKFTVTIQTPEKAYTYRLAPYGFNNKTRRWECLDTKYGTKRTYQADIFVATDEDIPESEMTEVYGTKDYIFILDFADLRTGVAFNGVTINPRNITMISFDCTEAHHGLGKDAYIAAMYNNDDGATFQMEIGGIHTNAALAAGDKLQCIWRYLDVNGNAQAAENEFEVVSYEGFGTSNFSVKCKGMLPGKFIGCDAFYGKYLQTDGPIKQVDSVKWFTNLTVSGSGRKQLGQRKYPQVVMGMGMTSGFDDGYNLTPERQVKMAYGLGYRDWWTTYIGMSHYWKGLTAFQDKETGELITEQTVLDYPILFAGESQVAIHFMSGAYPDRGYDVFQKYMTETWGINYAGVHPINGTTGSTAVDRACAVNPNSEVFDPTQSSGAGGLWWWDLEADKPGPALLHCVGQVGKLKPKAIIWGQGDQDATALAYPGDRNPAPSLTRTKQATKKVFEYLRSLYGQIPIFIQELSYAWGITNTDAPNVPIRTGLPSFLAARRNTWGDIEFRWKSYGLDPALAQYRIEIYNPSNLNQILHSFVVSGTQEANGYVYADFTVEDWIPVMMEAVGSPNPWEFMKWRVVCLYQEREIPSAPWSDNIPLDNAGLVKKTILVGINQFGGGHFTDMSDPTATTANGAIGRKDKVSASTLRLTFAEKAGLRPIQVMPVNVAADSAGMTVGTHKWWNTSSNSPGDALLAINDMVKGLGVKPDYFIEANPWETMYMKDVNSSTWPALMTAFESSNKAMLAWMRTNWGNPNLEIWFQGATTVWFGVAPPNDLNSEATVTVRDKQIQMATANIGFKLGSFVPGSNLYTAYRNVESSWIYYTVEAFHATAIELGEALALNINRATNPPDWSYLRPPANLQGRKLATRDIKMTWDNRAGITHWKYANRHVTTGAEISSGILTSPEYVFTLNDQQNAYNGDTLNMSFSVSEYAADSGAVGASSSFVGVVQNGSYMQTPTQLKAAKQLNGDIIFTWVGRPSWQHFWVVNTSVNDSKTVIFSKEWSSESLTWTVAEQNEFYGLEEGGATHVIFMVSEYDPSNGLVSIGAQVTGQAEQPSNPMNPVAGLYAVFTGDPGNSNIKIMWDKPSVGGRDVRIRNMHVTSSATISDQFVSDNNLVFTREEQVAAYGFTASSVSVRAQEHDIESGALGLTTEYVAVPETAGTVGQGFAKKDSVGNCTMSWEVGDAVQWQVEILNAENSTVVKTEIVVAPTITWMAEEITAEYGYLTDHMVWRVRPYRADGASNVAKQFDMTATL

Entity 3 polymer

description	Gp54
formula_weight	32438.4 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	TA,TB,TC,TD,TE,TF,TG,TH,TI,TJ,TK,TL

MSCGAELEANALLTALVAGEDFTLPDIDMSGSEYDIPGGINSPIYAEIEKITTEQLTTREVGGSGVFDALMQSASNHLLAEFKNNRITGGDYVKAYIATMEACMANAVQFLTTKDQAYWNAVTAQVAAITARANLGIIKANFVTAKIQALATKAEYALTKLKLSNESVTYCTAQYNLSSMLPQQLLMLKNQTTQVAEQTKLTTEQINMTKEQKEAQRAQTSDTRTDGTRVAGSVGKQKELYDQQITSYKRDAEVKAAKLFTDAWVTQKTIDEGLSPPNGFTNSSLDSILTALKNNNALG

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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	3.61 Å
resolution_method	—
num_particles	18434

fit	/app/data/saxs_computation/yf/9yft/9yft.fit
pddf	/app/data/pr_computation/yf/9yft/9yft.pr.out
profile	/app/data/saxs_computation/yf/9yft/9yft.dat

N4 Bacteriophage Asymmetric Tail Gating Complex

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

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)