SAXSdb — 9xqd

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1. Structure Basics

entry_id	9xqd
deposition_date	2025-11-18
title	The structure of outer peripheral region in the phage phiKZ baseplate complex
keywords	baseplate, outer peripheral, 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	98.46 Å
rg_electron	98.62 Å
i0	13629500000.00
molecular_weight	1007300.0 kDa
excluded_volume	1264000 Å³
envelope_volume	2460500 Å³
shell_volume	216840 Å³
envelope_diameter	336.2 Å
shell_rg	87.33 Å
envelope_rg	93.45 Å
shape_rg	98.61 Å
total_rg	98.56 Å
total_atoms	71157
n_residues	8852
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	262.3 Å
rg_real	94.66 Å
rg_real_error	0.75 Å
i0_real	1.3060e+10
i0_real_error	2.6290e+08
rg_reciprocal	97.51 Å
i0_reciprocal	13580000000.0000
total_estimate	0.9149
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	114.8 Å
skewness	0.179
kurtosis	-0.513
angular_range	— – 0.0800 Å⁻¹
current_alpha	0.8945
highest_alpha	403000000.0000
n_real_points	17
gnom_version	4.1.3
quality_criteria	AN1: 0.001; Oscil: 1.000; Stabil: 0.969; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.001

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	PHIKZ026
formula_weight	62047.6 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	a,b,c,d,e,f
atom_count	71157

MTTSYESSQYQPPQHKNHFWFRGDIVSYAGETGKAIPAKGDLVFDAAQGWFIVREVDETTGVSILDPWYMPQKPGNENEQNLLVAVGPGYSSESYRLFLDQSVTPFNICPDRRLHFYGSMVHGYKVFLGSDISEIHGKVISLFYDNAGNYLGPTIPVESVPDPLTQQNVVKALMNGRTAEKMQNGERVTLVAYDDVGGPVSIAQLVVMNTEVIAQEDTSKKYVGGITIESPFISPADPKVIEFPLNVPVESLPMMGAVHYRDGKKHVMNIDGTAMAIYGLRNYIATEEGQEFKLTLSYQLAQDELSYLSTPSANRRIQETYTARTTPVQGAYSCRMFVYPAWVNEAVGYRLEFWLANIDRQQIWNITPYVELGANSAPFNPRGYGTIQTLTYAVNLNQVDGRFLPVRFASTFQVALLSAGNNRNANWEIYSRPDQGEAYGRDLKADIEFINGNLWDLRLANGAQSQAAWLKKMYFAAEPLTGPMEATPPTPTHFRVRTVHNEYEYTVSQWNTALRINAQDMADGALLQITWIRREYDTDLQLAITALPCLQR

Entity 2 polymer

description	PHIKZ027
formula_weight	105364.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,K

MNAYLLRHAIDNVWCNPAQDRQFVYELKQLTPRYGVRVNWVVDYTRYKLPVQSTRDYWHLYQIGKMIPKHLGLPKVYNKWMSLNELAQNHLNLADVYVNSGINYSRNDTYVLITSSQNLLIAVKIDPLFPDLDENQPYLHVYNNAYFQSNRSDVAGHRWLVSESYRVKTISELTQFQIKIMDTIASKGGVPKYFVNGRYVNEISPVTATVGDVCDFILDPSIKRMVDFDLRTLPVFMSEIDSERKYILHYTDKTVQTIEFFDDVEAYIYQPLGNNRYTGVNYHHNESRWMRMLTHKDYSIPTARIDQFKALHPEDPRRGADPTRWPSQNWKALDNLVFRIYIHHSGYDRPLVADSHRIQILYRLKSEDIIRAMTGADSGNPLWRAENLEQSPYCWFMSAPSSFVYPLTFNLPEETSPSKVEAQNMAGDVFGYYEAANIQGYNPAWVYNDAGLKTADLRYNYWLDATVFEYDEKGILLGYNYHTAGRKYFPKDSRCAYVECINGKGSVDLHEAYGNDPVPLRDGDNWRVYVSPVWAGVPTGEWQDITDHPDRNNWGFYDDTTDDKRWVWIAKSNEWYGLVRTDEYFYLKELKFNKTDGIIKWSIRNTETHNGVKVDKLMEIPFGQYDVFVNGRPIIEGLDYTREWPQTVLCNLEYLNADPNAVNTILLRGTGFPTPDLKPYEPGEIGFIEYGVLSNDGIYKVHSNKQSRIIIDGHYRDPADLEFQEDQGTTVITDERNGAPFQIQTPQARFRDVYNDDYQARIKDDARDKQVTDFMTEYFPMKPQPNPDKIDYRYQVLSAFSCKIIHDIVKEYIKPPYQNGRYSDDDIVKQLKDYEWLAAYDIINKGYNKNKVVVYPHWYTEPVELDIFQWEYLNRILSIYLREVPPLSLFVKIKRNQP

Entity 3 polymer

description	PHIKZ127
formula_weight	33643.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	0

MFITRDYCKVDPWTAIVEMINNNYMYQLTPGTCKLLEFEAIDHKRTRIKIDPCRDNKPGELLPVVERTEFFYQRLDFNEFFKVPQVVEVKDVYLPFTTLDLAKLICEKNDIKFDLDDFYHQEINSYNQDVTITCNPDSLRFVGEFKIKLINTVRQDISLLTKVNSFPTIVKWPAGNGNKPTAEFITMSLDFTDYRSFLLPIKAFKENPYSLEMAAILKKVTGLDFVAKSNATDYNITNIVRNGVNNFIVDYNGPVVPAYSLRNDITNVMVLRLSKTMCPNINGRLLIHYN

Entity 4 polymer

description	PHIKZ130
formula_weight	48651.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,H

MYTLVRSRHRIDRKSGRWTDVDLANEKISTLSVKFGDIYLYIEYPGPTAPILNALHWVNVTNEISSANPDLTVQEWLTSLGDKSLPFDDELPNEKVRLVKYAQAWHAGYIAQPVARNGHVTDGGSKFKKEDILLTHPKHKPEDVCRKCLITVNTMFHLADYTSAGVRIIDGNKTVRTANDNQIGLYSFETIGDIKYVPIKTDMIYPQQVGAPLFDATYIDMPEDIDLTNKTILLSLGGYLCVLGKGFNRVGVRTWRVDFGSLSMFDRYMQSRELIDLSSLGLEIDDKNKTLLSVEQIKKDSVIKAYMTLSQTFFIVLDSPSLFQEFVPLEPLKLPGRYQATNTRTEVYPKYTKPDQLPVVGAHGKMLDYHFIHEDKHSVYCCTLNIRNNFDAHTHDWKTEKVVDGGRYPAWPFVHDTAYLRILGVDG

Entity 5 polymer

description	PHIKZ139
formula_weight	32691.9 kDa
src_method	nat
entity_count	6

Polymer

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

MSAIDQQYINVTRTAYGSYLQTCKYLGIPFKLIPNTTLNEKFSIQQNVAPSAGQIPNVQYMVIGNRGHYFVKGPDGSDEVENNIHRANDAALYNHIPFVLREVADDLPAQRRNMYRLRRLEEHNGKQYFAYYARKIDVTGVVPKLLKITIVDGEPVVTPYVPNRDDLNPTPPTISNQGTVVGSNESISASAIVTVNLTAEEILEITTAHRIRTGSVRSPIISEIGLCSGVDKDVQGQSGASGNFIYTEVIACQINVFIATNHAVGYNSDGLKLTFDIGGVEPMLGSKAINVAKFVPKD

Entity 6 polymer

description	PHIKZ157
formula_weight	51155.7 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	J,P,T,V,N,R

MYNLKGFYEYPSLIDNATDKVAKFGEISDNSATYAKDKKILTSESTPSTAFIAFHSVRDEIPVDITAEYQLQVLKIGEFLLKQGNSGTIGKNTTPTQVNQMLMTEFNGKLSTVRSGPIGNMNTRLYLPEYIEFSLIVTGNEPNLIRVWLADDAFAGQYDEFKIEVVHPIGKNAQGNYDDWFKDPLEVKKLLDKFDLPTKLEEVQAKRAQYPYTYQNAYRFDYHNPRDDTMQFPAYWIVIIYGVAGNNLDIIKDAICDELLDGSAHTREEWEKILPELFRTTEFIICPFWNQLALENSDFRGGIYSPIIDPRKRIALMRRTARGSGYTTTYFDSHYELSCNIYRSVGFSVIGNAKNRNNLTQFSQVFPDYIIATNTSEDINRISVETREFLLVFADLLKAAEDMDRYTTVPMGMSRMIRDDVIYAAKVYKNINYMVVTRKSVEQFG

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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	4.530 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.53 Å
resolution_method	—
num_particles	131125

fit	/app/data/saxs_computation/xq/9xqd/9xqd.fit
pddf	/app/data/pr_computation/xq/9xqd/9xqd.pr.out
profile	/app/data/saxs_computation/xq/9xqd/9xqd.dat

The structure of outer peripheral region in the phage phiKZ baseplate 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

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)