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9xy8

One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence

Method: X-RAY DIFFRACTION D_max: 91.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xy8
deposition_date	2025-08-25
last_revision	2025-09-10
title	One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence
keywords	meganuclease, structure prediction, protein engineering, DNA BINDING PROTEIN-DNA complex, DNA BINDING PROTEIN; 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	25.15 Å
rg_electron	24.12 Å
i0	56621200.00
molecular_weight	49565.0 kDa
excluded_volume	58066 Å³
envelope_volume	70885 Å³
shell_volume	25516 Å³
envelope_diameter	94.8 Å
shell_rg	30.53 Å
envelope_rg	24.48 Å
shape_rg	24.05 Å
total_rg	24.92 Å
total_atoms	3442
n_residues	348
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	91.5 Å
rg_real	25.33 Å
rg_real_error	0.76 Å
i0_real	5.6620e+07
i0_real_error	8.6530e+05
rg_reciprocal	25.28 Å
i0_reciprocal	56620000.0000
total_estimate	0.8046
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.1 Å
skewness	0.601
kurtosis	-0.024
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	7278000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.606; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.681; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	eI-OnuI_P456_CCC
formula_weight	34447.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3532

MASSRRESINPWILTGFADAEGSFLLRIRNNNKSSVGYSTELGFQITLHNKDKSILENIQSTWKVGVIANSGDNAVSLKVTRFEDLKVIIDHFEKYPLITQKLGDYKLFKQAFSVMENKEHLKENGIKELVRIKAKLNWGLTDELKKAFPENISKERSLINKNIPNFKWLAGFTSGEGTFGVNLIKSKSKLGVQVQLRFSITQHIKDKNLMNSLITYLGCGYIKERNKSEFSWLEFVVTKFSDINDKIIPVFQENTLIGVKLEDFEDWCKVAKLIEEKKHLTESGLDEIKKIKLNMNKGR

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (26-MER)
formula_weight	7895.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GGGTTTCCACTTATTCACCCTTTTAG

Entity 3 polymer

description	DNA (26-MER)
formula_weight	8078.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

CCTAAAAGGGTGAATAAGTGGAAACC

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	90

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6. Citations (1)

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length_a	39.222 Å
length_b	76.159 Å
length_c	167.753 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.490 Å
resolution_low	45.073 Å
r_factor	0.1988
r_work	0.1930
r_free	0.2495

fit	/app/data/saxs_computation/xy/9xy8/9xy8.fit
pddf	/app/data/pr_computation/xy/9xy8/9xy8.pr.out
profile	/app/data/saxs_computation/xy/9xy8/9xy8.dat

One of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)