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9yzk

Isoreticular co-crystal 1 with symmetrical expanded duplex (42mer) containing insert sequence ACCCTTCTATGACCTACTCCA

Method: X-RAY DIFFRACTION D_max: 89.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yzk
deposition_date	2025-10-30
last_revision	2026-02-18
title	Isoreticular co-crystal 1 with symmetrical expanded duplex (42mer) containing insert sequence ACCCTTCTATGACCTACTCCA
keywords	Protein-DNA complex, DNA Binding protein, Transcription factor, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	34.02 Å
rg_electron	32.79 Å
i0	73146500.00
molecular_weight	49164.0 kDa
excluded_volume	53537 Å³
envelope_volume	83087 Å³
shell_volume	25395 Å³
envelope_diameter	144.1 Å
shell_rg	32.05 Å
envelope_rg	34.46 Å
shape_rg	32.54 Å
total_rg	33.25 Å
total_atoms	3359
n_residues	308
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	89.5 Å
rg_real	30.85 Å
rg_real_error	0.23 Å
i0_real	6.9310e+07
i0_real_error	8.7240e+05
rg_reciprocal	34.30 Å
i0_reciprocal	73120000.0000
total_estimate	0.6765
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	30.5 Å
skewness	0.381
kurtosis	-0.615
angular_range	— – 0.2350 Å⁻¹
current_alpha	1.4590
highest_alpha	1829000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.006; Oscil: 0.992; Stabil: 0.983; Sysdev: 0.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Replication initiation protein
formula_weight	30749.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	3367

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

Source

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

Entity 2 polymer

description	DNA (42-MER)
formula_weight	12706.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

AGTATCTTCCCACCTGTGACAAATTGCCCTCAGACCTCATCC

Entity 3 polymer

description	DNA (42-MER)
formula_weight	13155.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

CTGGATGAGGTCTGAGGGCAATTTGTCACAGGTGGGAAGATA

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	75.836 Å
length_b	163.022 Å
length_c	192.278 Å
angle_alpha	90.00 °
angle_beta	98.61 °
angle_gamma	90.00 °
z_pdb	4

space_group	I 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	5.100 Å
resolution_low	47.530 Å
r_factor	0.2790
r_work	0.2763
r_free	0.3040

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

Isoreticular co-crystal 1 with symmetrical expanded duplex (42mer) containing insert sequence ACCCTTCTATGACCTACTCCA

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

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)