SAXSdb — 9yf5

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1. Structure Basics

entry_id	9yf5
deposition_date	2025-09-25
title	N4 Empty Particle C6 Tail
keywords	dodecamer, bacteriophage portal, 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	— Å
rg_electron	119.40 Å
i0	117064000000.00
molecular_weight	2940500.0 kDa
excluded_volume	3681100 Å³
envelope_volume	6342200 Å³
shell_volume	449500 Å³
envelope_diameter	455.0 Å
shell_rg	110.30 Å
envelope_rg	117.70 Å
shape_rg	119.40 Å
total_rg	119.20 Å
total_atoms	207084
n_residues	26124
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	354.8 Å
rg_real	113.90 Å
rg_real_error	1.58 Å
i0_real	1.1260e+11
i0_real_error	2.4960e+09
rg_reciprocal	109.90 Å
i0_reciprocal	113600000000.0000
total_estimate	0.8863
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	109.2 Å
skewness	0.540
kurtosis	-0.183
angular_range	— – 0.0650 Å⁻¹
current_alpha	0.8622
highest_alpha	58640000000.0000
n_real_points	14
gnom_version	4.1.3
quality_criteria	AN1: 0.005; Oscil: 0.881; Stabil: 0.967; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.027

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	30 kDa protein
formula_weight	27192.4 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL
atom_count	207084

MYYIEELFCRLANGVLNNTGIVTDDRGDIEDDSKPFIIVAANEALTRLHGRFNMRNNNVVVEMQEGRTNYPLLAKYAVQSYDPNEVKCPFIMDLAGEKFAEDVIRILEVYDDKGRRRPLNDRNNPCSLFTPRPNVLQNNAPKAWEVLNVMYQAKHPKLSTAEDGYNEIDIPDTLDPALDAYIAYRYYTSLNTPESSAKAAEYLSFYDSICREVVEYDLTSDTEVDTNTLFRKRGWR

Entity 2 polymer

description	Non-contractile tail sheath
formula_weight	154255.1 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	LA,LB,LC,LD,LE,LF

MSIEDYLKGKNCLASPNYDPDDQHSSWREDLPQFKKDREHLTLVNTRRNRTYNTKLNRFDPEYWVVDYNALMVATIIPYGSKSFKVPCQWRTNKDFLGVRWMTEDTFDHHLYRYETDPNYLGLILAFRHNPDEPDKFTVTIQTPEKAYTYRLAPYGFNNKTRRWECLDTKYGTKRTYQADIFVATDEDIPESEMTEVYGTKDYIFILDFADLRTGVAFNGVTINPRNITMISFDCTEAHHGLGKDAYIAAMYNNDDGATFQMEIGGIHTNAALAAGDKLQCIWRYLDVNGNAQAAENEFEVVSYEGFGTSNFSVKCKGMLPGKFIGCDAFYGKYLQTDGPIKQVDSVKWFTNLTVSGSGRKQLGQRKYPQVVMGMGMTSGFDDGYNLTPERQVKMAYGLGYRDWWTTYIGMSHYWKGLTAFQDKETGELITEQTVLDYPILFAGESQVAIHFMSGAYPDRGYDVFQKYMTETWGINYAGVHPINGTTGSTAVDRACAVNPNSEVFDPTQSSGAGGLWWWDLEADKPGPALLHCVGQVGKLKPKAIIWGQGDQDATALAYPGDRNPAPSLTRTKQATKKVFEYLRSLYGQIPIFIQELSYAWGITNTDAPNVPIRTGLPSFLAARRNTWGDIEFRWKSYGLDPALAQYRIEIYNPSNLNQILHSFVVSGTQEANGYVYADFTVEDWIPVMMEAVGSPNPWEFMKWRVVCLYQEREIPSAPWSDNIPLDNAGLVKKTILVGINQFGGGHFTDMSDPTATTANGAIGRKDKVSASTLRLTFAEKAGLRPIQVMPVNVAADSAGMTVGTHKWWNTSSNSPGDALLAINDMVKGLGVKPDYFIEANPWETMYMKDVNSSTWPALMTAFESSNKAMLAWMRTNWGNPNLEIWFQGATTVWFGVAPPNDLNSEATVTVRDKQIQMATANIGFKLGSFVPGSNLYTAYRNVESSWIYYTVEAFHATAIELGEALALNINRATNPPDWSYLRPPANLQGRKLATRDIKMTWDNRAGITHWKYANRHVTTGAEISSGILTSPEYVFTLNDQQNAYNGDTLNMSFSVSEYAADSGAVGASSSFVGVVQNGSYMQTPTQLKAAKQLNGDIIFTWVGRPSWQHFWVVNTSVNDSKTVIFSKEWSSESLTWTVAEQNEFYGLEEGGATHVIFMVSEYDPSNGLVSIGAQVTGQAEQPSNPMNPVAGLYAVFTGDPGNSNIKIMWDKPSVGGRDVRIRNMHVTSSATISDQFVSDNNLVFTREEQVAAYGFTASSVSVRAQEHDIESGALGLTTEYVAVPETAGTVGQGFAKKDSVGNCTMSWEVGDAVQWQVEILNAENSTVVKTEIVVAPTITWMAEEITAEYGYLTDHMVWRVRPYRADGASNVAKQFDMTATL

Entity 3 polymer

description	Gp64
formula_weight	48100.7 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	SA,SB,SC,SD,SE,SF

MSNAAVVPMPYSPTTVPREQIREIQLQLINEMTDVHMGALTAQYMPDDFTFEPGIGQIHFNVETSRKVCLDLAKSVLRLVPVYPLVSPVKKQHDDYWFVGRLGLDPVSEPEPINMPTMEFYKRFLSLLHERDMKFVNSVAYEILNFFMPDEWKQLNWKGDPALSGWYPPSSFIQPTNKDALDFVSKAQCQILKECQNLGMELYFQIGEPWWWDGSYNTGEGKNAPCIYDPKTMALYKEETGNDVPTPWIKDIFAPVEEHQWPYVDWLCTKLGQSTNYIRDYVKGKFPDAQATLLFFTPQIMSPASELTGRLNFPESEWIFPNYDFVQIEDYDWIIDGRLDLVPLTFDAAVNRLGYPLNVVHYFIGFVLLPEDAKKIWADVDKAWGLALEAGIPHIYPWSYTQVMRDGVIYAVPKVCG

Entity 4 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

Entity 5 polymer

description	60 kDa protein
formula_weight	58943.9 kDa
src_method	nat
entity_count	36

Polymer

type	polypeptide(L)
strand_id	XA,XB,YA,YB,ZA,ZB,XC,XD,YC,YD,ZC,ZD,XE,XF,YE,YF,ZE,ZF,XG,XH,YG,YH,ZG,ZH,XI,XJ,YI,YJ,ZI,ZJ,XK,XL,YK,YL,ZK,ZL

MSGHTPFNTIPNEGYCCETLNDPIVDKMIGNAYYVVKFVALRMPFIKNVSDNMTQLLAIHNKLTELSAIYTKLDELQLIHNNLDKLQELYNQLSKLTGLYDNLQALLRVYDNLTPINTVASNIDAVNTVATDIAKVIIVSAQIDKVITVANSITNVNTVAGSIDAVNTVSTNINAIKNVNTNMAALLDLDNHMTELLAVHARLGDLVTIAEQLDTIIADHEKYATAEGAGLIGFNQAQTYAANTVGAMLRQVITMGNDKGGYAVAGKLTSARGVWSLATGSINMNAPTAGAVANLVLNYKAGKVSGLLVAPSQQMALDGLIMGASTADNTATVSVTAPLRFKADLTAKTISGVNTRIMPSSAVTLNVDAYGGITLGYPPSLQTVEPVMTFITPTGKAPLTPRFSSVTAGAAVLVMVGEAEAQLKYSGGGWAAVSDWDSGTYCAFDTVSGELTVYHSTLIKDSTVTFSLLLPTDDTQLTAQLKSHTDSSFVVKIAKPDGSLLDAPLEGMGIMYSRGMHGIYKVPYGSLIVDVGRVQVKFSEFNTTEGISVVGINSNA

Entity 6 polymer

description	Probable portal protein
formula_weight	85642.5 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	PA,PB,PC,PD,PE,PF,PG,PH,PI,PJ,PK,PL

MEQNTDSMVPLPDPSQATKLTSWKNELSLQALKADLDAAKPSHTAMMIKVKEWNDLMRIEGKAKPPKVKGRSQVQPKLVRRQAEWRYSALTEPFLGSNKLFKVTPVTWEDVQGARQNELVLNYQFRTKLNRVSFIDNYVRSVVDDGTGIVRVGWNREIRKEKQEVPVFSLFPIQTQEQADALQQALQLRTDNPRGYEENVDEAIKESVRFFDETGQATYAVQTGTTTTEVEVPLANHPTVEMLNPENIIIDPSCQGDINKAMFAIVSFETCKADLLKEKDRYHNLNKIDWQSSAPVNEPDHATTTPQEFQISDPMRKRVVAYEYWGFWDIEGNGVLEPIVATWIGSTLIRLEKNPYPDGKLPFVLIPYMPVKRDMYGEPDAELLGDNQAVLGAVMRGMIDLLGRSANGQRGMPKGMLDALNSRRYREGEDYEYNPTQNPAQMIIEHKFPELPQSALTMATLQNQEAESLTGVKAFAGGVTGESYGDVAAGIRGVLDAASKREMAILRRLAKGMSEIGNKIIAMNAVFLAEHEVVRITNEEFVTIKREDLKGNFDLEVDISTAEVDNQKSQDLGFMLQTIGPNVDQQITLNILAEIADLKRMPKLAHDLRTWQPQPDPVQEQLKQLAVEKAQLENEELRSKIRLNDAQAQKAMAERDNKNLDYLEQESGTKHARDLEKMKAQSQGNQQLEITKALTKPRKEGELPPNLSAAIGYNALTNGEDTGIQSVSERDIAAEANPAYSLGSSQFDPTRDPALNPGIRLGN

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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	3.65 Å
resolution_method	—
num_particles	10265

fit	/app/data/saxs_computation/yf/9yf5/9yf5.fit
pddf	/app/data/pr_computation/yf/9yf5/9yf5.pr.out
profile	/app/data/saxs_computation/yf/9yf5/9yf5.dat

N4 Empty Particle C6 Tail

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 (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)