SAXSdb — 9yxm

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1. Structure Basics

entry_id	9yxm
deposition_date	2025-10-27
title	10-23 DNAzyme in complex with T7 RNA Polymerase
keywords	10-23 DNAzyme, RNA cleavage, T7 RNA Polymerase, Scaffold, DNA; DNA
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	36.94 Å
rg_electron	35.09 Å
i0	212863000.00
molecular_weight	105220.0 kDa
excluded_volume	126680 Å³
envelope_volume	174940 Å³
shell_volume	44286 Å³
envelope_diameter	139.3 Å
shell_rg	39.14 Å
envelope_rg	35.22 Å
shape_rg	34.95 Å
total_rg	35.76 Å
total_atoms	7329
n_residues	834
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	133.0 Å
rg_real	37.30 Å
rg_real_error	1.21 Å
i0_real	2.1290e+08
i0_real_error	3.6900e+06
rg_reciprocal	37.08 Å
i0_reciprocal	212800000.0000
total_estimate	0.8096
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.3 Å
skewness	0.664
kurtosis	0.273
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	10360000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.851; Smooth: 0.723

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	RNA polymerase
formula_weight	99813.1 kDa
ec_number	2.7.7.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7329

MNTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFAHHHHHH

Source

organism	Escherichia phage T7
ncbi_taxonomy_id	10760
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	DNA (44-MER)
formula_weight	13533.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

TGGCGAAAGGCTAGCTACAACGAATTCTAATACGACTCACTATA

Entity 3 polymer

description	;DNA/RNA (5'-D(PTPAPGPTPGPAPGPTPCPGPTPAPTPTPAPGPAPAPT)-R(PA)-D(PTPTP*T)-3') ;
formula_weight	10728.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide/polyribonucleotide hybrid
strand_id	C

CTCCCTATAGTGAGTCGTATTAGAATATTTCGCCA

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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	4.62 Å
resolution_method	—
num_particles	10059

fit	/app/data/saxs_computation/yx/9yxm/9yxm.fit
pddf	/app/data/pr_computation/yx/9yxm/9yxm.pr.out
profile	/app/data/saxs_computation/yx/9yxm/9yxm.dat

10-23 DNAzyme in complex with T7 RNA Polymerase

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

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)