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9yzd

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC

Method: X-RAY DIFFRACTION D_max: 101.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yzd
deposition_date	2025-10-30
last_revision	2026-02-18
title	Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC
keywords	Protein-DNA complex, DNA binding protein, Transcription factor; DNA BINDING PROTEIN
method	X-RAY DIFFRACTION

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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	28.14 Å
rg_electron	26.87 Å
i0	51545800.00
molecular_weight	43980.0 kDa
excluded_volume	49722 Å³
envelope_volume	67322 Å³
shell_volume	23420 Å³
envelope_diameter	106.6 Å
shell_rg	30.20 Å
envelope_rg	27.71 Å
shape_rg	26.72 Å
total_rg	27.49 Å
total_atoms	3020
n_residues	278
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	101.3 Å
rg_real	28.64 Å
rg_real_error	1.10 Å
i0_real	5.1550e+07
i0_real_error	8.8360e+05
rg_reciprocal	28.49 Å
i0_reciprocal	51540000.0000
total_estimate	0.7961
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.9 Å
skewness	0.706
kurtosis	0.113
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	2783000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.566; Smooth: 0.795

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA (31-MER)
formula_weight	9472.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	3040

CCTGTGACAAATTGCCCTCAGCTAATTAGGC

Entity 2 polymer

description	DNA (31-MER)
formula_weight	9592.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GGCCTAATTAGCTGAGGGCAATTTGTCACAG

Entity 3 polymer

description	Replication initiation protein
formula_weight	30749.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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6. Citations (2)

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length_a	76.032 Å
length_b	124.855 Å
length_c	139.093 Å
angle_alpha	90.00 °
angle_beta	91.85 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.090 Å
resolution_low	45.290 Å
r_factor	0.2546
r_work	0.2535
r_free	0.2645

fit	/app/data/saxs_computation/yz/9yzd/9yzd.fit
pddf	/app/data/pr_computation/yz/9yzd/9yzd.pr.out
profile	/app/data/saxs_computation/yz/9yzd/9yzd.dat

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC

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

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)