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9z55

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

Method: X-RAY DIFFRACTION D_max: 100.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z55
deposition_date	2025-11-11
last_revision	2026-02-18
title	Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT
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	28.03 Å
rg_electron	27.13 Å
i0	49571600.00
molecular_weight	41457.0 kDa
excluded_volume	45993 Å³
envelope_volume	66184 Å³
shell_volume	23070 Å³
envelope_diameter	105.0 Å
shell_rg	30.18 Å
envelope_rg	27.48 Å
shape_rg	26.99 Å
total_rg	27.71 Å
total_atoms	2842
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	100.1 Å
rg_real	28.49 Å
rg_real_error	0.93 Å
i0_real	4.9570e+07
i0_real_error	7.2060e+05
rg_reciprocal	28.35 Å
i0_reciprocal	49570000.0000
total_estimate	0.8129
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.9 Å
skewness	0.686
kurtosis	0.086
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	2635000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.692; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.643; Smooth: 0.845

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	2862

CCTGTGACAAATTGCCCTCAGCATGAGTCAT

Entity 2 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	B

GATGACTCATGCTGAGGGCAATTTGTCACAG

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)

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6. Citations (2)

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length_a	146.484 Å
length_b	129.876 Å
length_c	73.317 Å
angle_alpha	90.00 °
angle_beta	118.58 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.940 Å
resolution_low	64.940 Å
r_factor	0.2988
r_work	0.2968
r_free	0.3161

fit	/app/data/saxs_computation/z5/9z55/9z55.fit
pddf	/app/data/pr_computation/z5/9z55/9z55.pr.out
profile	/app/data/saxs_computation/z5/9z55/9z55.dat

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

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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)