SAXSdb — 9pnt

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1. Structure Basics

entry_id	9pnt
deposition_date	2025-07-21
last_revision	2025-12-10
title	N4 vRNAP gp50 - open complex
keywords	Single Subunit RNA Polymerase, Bacteriophage Ejection Protein, VIRAL PROTEIN, TRANSFERASE; VIRAL PROTEIN, TRANSFERASE
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	50.81 Å
rg_electron	50.66 Å
i0	1071710000.00
molecular_weight	270680.0 kDa
excluded_volume	338550 Å³
envelope_volume	505940 Å³
shell_volume	83122 Å³
envelope_diameter	162.0 Å
shell_rg	54.19 Å
envelope_rg	49.59 Å
shape_rg	50.66 Å
total_rg	50.77 Å
total_atoms	19009
n_residues	2444
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	162.4 Å
rg_real	50.81 Å
rg_real_error	1.15 Å
i0_real	1.0720e+09
i0_real_error	1.8510e+07
rg_reciprocal	50.79 Å
i0_reciprocal	1072000000.0000
total_estimate	0.8733
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.4 Å
skewness	0.267
kurtosis	-0.670
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	143300000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.541

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Virion DNA-directed RNA polymerase
formula_weight	382903.5 kDa
ec_number	2.7.7.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	19009

MSVFDRLAGFADSVTNAKQVDVSTATAQKKAEQGVTTPLVSPDAAYQMQAARTGNVGANAFEPGTVQSDFMNLTPMQIMNKYGVEQGLQLINARADAGNQVFNDSVTTRTPGEELGDIATGVGLGFVNTLGGIGALGAGLLNDDAGAVVAQQLSKFNDAVHATQSQALQDKRKLFAARNLMNEVESERQYQTDKKEGTNDIVASLSKFGRDFVGSIENAAQTDSIISDGLAEGVGSLLGAGPVLRGASLLGKAVVPANTLRSAALAGAIDAGTGTQSLARIASTVGRAAPGMVGVGAMEAGGAYQQTADEIMKMSLKDLEKSPVYQQHIKDGMSPEQARRQTASETGLTAAAIQLPIAAATGPLVSRFEMAPFRAGSLGAVGMNLARETVEEGVQGATGQLAQNIAQQQNIDKNQDLLKGVGTQAGLGALYGFGSAGVVQAPAGAARLAGAATAPVLRTTMAGVKAAGSVAGKVVSPIKNTLVARGERVMKQNEEASPVADDYVAQAAQEAMAQAPEAEVTIRDAVEATDATPEQKVAAHQYVSDLMNATRFNPENYQEAPEHIRNAVAGSTDQVQVIQKLADLVNTLDESNPQALMEAASYMYDAVSEFEQFINRDPAALDSIPKDSPAIELLNRYTNLTANIQNTPKVIGALNVINRMINESAQNGSLNVTEESSPQEMQNVALAAEVAPEKLNPESVNVVLKHAADGRIKLNNRQIAALQNAAAILKGAREYDAEAARLGLRPQDIVSKQIKTDESRTQEGQYSALQHANRIRSAYNSGNFELASAYLNDFMQFAQHMQNKVGALNEHLVTGNADKNKSVHYQALTADREWVRSRTGLGVNPYDTKSVKFAQQVALEAKTVADIANALASAYPELKVSHIKVTPLDSRLNAPAAEVVKAFRQGNRDVASSQPKADSVNQVKETPVTKQEPVTSTVQTKTPVSESVKTEPTTKESSPQAIKEPVNQSEKQDVNLTNEDNIKQPTESVKETETSTKESTVTEELKEGIDAVYPSLVGTADSKAEGIKNYFKLSFTLPEEQKSRTVGSEAPLKDVAQALSSRARYELFTEKETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGTEANRWVGGKLLNIVEQDGDTFKYNEQLLQTAVLAGLQWRLTATSNTAIKDAKDVAAITGIDQALLPEGLVEQFDTGMTLTEAVSSLAQKIESYWGLSRNPNAPLGYTKGIPTAMAAEILAAFVESTDVVENIVDMSEIDPDNKKTIGLYTITELDSFDPINSFPTAIEEAVLVNPTEKMFFGDDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGTLNKELLNDNHAKSLEGKNRSVEDSYNQLFSVIEQVRAQSEDISTVPIHYAYNMTRVGRMQMLGKYNPQSAKLVREAILPTKATLDLSNQNNEDFSAFQLGLAQALDIKVHTMTREVMSDELTKLLEGNLKPAIDMMVEFNTTGSLPENAVDVLNTALGDRKSFVALMALMEYSRYLVAEDKSAFVTPLYVEADGVTNGPINAMMLMTGGLFTPDWIRNIAKGGLFIGSPNKTMNEHRSTADNNDLYQASTNALMESLGKLRSNYASNMPIQSQIDSLLSLMDLFLPDINLGENGALELKRGIAKNPLTITIYGSGARGIAGKLVSSVTDAIYERMSDVLKARAKDPNISAAMAMFGKQAASEAHAEELLARFLKDMETLTSTVPVKRKGVLELQSTGTGAKGKINPKTYTIKGEQLKALQENMLHFFVEPLRNGITQTVGESLVYSTEQLQKATQIQSVVLEDMFKQRVQEKLAEKAKDPTWKKGDFLTQKELNDIQASLNNLAPMIETGSQTFYIAGSENAEVANQVLATNLDDRMRVPMSIYAPAQAGVAGIPFMTIGTGDGMMMQTLSTMKGAPKNTLKIFDGMNIGLNDITDASRKANEAVYTSWQGNPIKNVYESYAKFMKNVDFSKLSPEALEAIGKSALEYDQRENATVDDIANAASLIERNLRNIALGVDIRHKVLDKVNLSIDQMAAVGAPYQNNGKIDLSNMTPEQQADELNKLFREELEARKQKVAKARAEVKEETVSEKEPVNPDFGMVGREHKASGVRILSATAIRNLAKISNLPSTQAATLAEIQKSLAAKDYKIIYGTPTQVAEYARQKNVTELTSQEMEEAQAGNIYGWTNFDDKTIYLVSPSMETLIHELVHASTFEEVYSFYQGNEVSPTSKQAIENLEGLMEQFRSLDISKDSPEMREAYADAIATIEGHLSNGFVDPAISKAAALNEFMAWGLANRALAAKQKRTSSLVQMVKDVYQAIKKLIWGRKQAPALGEDMFSNLLFNSAILMRSQPTTQAVAKDGTLFHSKAYGNNERLSQLNQTFDKLVTDYLRTDPVTEVERRGNVANALMSATRLVRDVQSHGFNMTAQEQSVFQMVTAALATEAAIDPHAMARAQELYTHVMKHLTVEHFMADPDSTNPADRYYAQQKYDTISGANLVEVDAKGRTSLLPTFLGLAMVNEELRSIIKEMPVPKADKKLGNDIDTLLTNAGTQVMESLNRRMAGDQKATNVQDSIDALSETIMAAALKRESFYDAVATPTGNFIDRANQYVTDSIERLSETVIEKADKVIANPSNIAAKGVAHLAKLTAAIASEKQGEIVAQGVMTAMNQGKVWQPFHDLVNDIVGRTKTNANVYDLIKLVKSQISQDRQQFREHLPTVIAGKFSRKLTDTEWSAMHTGLGKTDLAVLRETMSMAEIRDLLSSSKKVKDEISTLEKEIQNQAGRNWNLVQKKSKQLAQYMIMGEVGNNLLRNAHAISRLLGERITNGPVADVAAIDKLITLYSLELMNKSDRDLLSELAQSEVEGMEFSIAYMVGQRTEEMRKAKGDNRTLLNHFKGYIPVENQQGVNLIIADDKEFAKLNSQSFTRIGTYQGSTGFRTGSKGYYFSPVAARAPYSQGILQNVRNTAGGVDIGTGFTLGTMVAGRITDKPTVERITKALAKGERGREPLMPIYNSKGQVVAYEQSVDPNMLKHLNQDNHFAKMVGVWRGRQVEEAKAQRFNDILIEQLHAMYEKDIKDSSANKSQYVNLLGKIDDPVLADAINLMNIETRHKAEELFGKDELWVRRDMLNDALGYRAASIGDVWTGNSRWSPSTLDTVKKMFLGAFGNKAYHVVMNAENTIQNLVKDAKTVIVVKAVVVPAVNFLANIYQMIGRGVPVKDIAVNIPRKTSEINQYIKSRLRQIDAEAELRAAEGNPNLVRKLKTEIQSITDSHRRMSIWPLIEAGEFSSIADAGISRDDLLVAEGKIHEYMEKLANKLPEKVRNAGRYALIAKDTALFQGIQKTVEYSDFIAKAIIYDDLVKRKKKSSSEALGQVTEEFINYDRLPGRFRGYMESMGLMWFYNFKIRSIKVAMSMIRNNPVHSLIATVVPAPTMFGNVGLPIQDNMLTMLAEGRLDYSLGFGQGLRAPTLNPWFNLTH

Source

organism	Escherichia phage N4
ncbi_taxonomy_id	2886925
host_organism	Escherichia coli

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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	4.30 Å
resolution_method	—
num_particles	18762

fit	/app/data/saxs_computation/pn/9pnt/9pnt.fit
pddf	/app/data/pr_computation/pn/9pnt/9pnt.pr.out
profile	/app/data/saxs_computation/pn/9pnt/9pnt.dat

N4 vRNAP gp50 - open 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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)