← Back to search

9xy2

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

Method: X-RAY DIFFRACTION D_max: 90.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9xy2
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

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	24.87 Å
rg_electron	23.89 Å
i0	56678600.00
molecular_weight	49886.0 kDa
excluded_volume	58621 Å³
envelope_volume	71593 Å³
shell_volume	25812 Å³
envelope_diameter	94.1 Å
shell_rg	30.53 Å
envelope_rg	24.28 Å
shape_rg	23.83 Å
total_rg	24.71 Å
total_atoms	3483
n_residues	345
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

▼

3. P(r) Analysis (GNOM)

dmax	90.3 Å
rg_real	25.08 Å
rg_real_error	0.81 Å
i0_real	5.6680e+07
i0_real_error	8.8510e+05
rg_reciprocal	25.03 Å
i0_reciprocal	56680000.0000
total_estimate	0.7366
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	25.8 Å
skewness	0.589
kurtosis	-0.024
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	8178000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.617; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.721; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	eI-OnuI_P456_AAC
formula_weight	34588.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3680

MASSRRESINPWILTGFADAEGSFLLRIRNNNKSSVGYSTELGFQITLHNKDKSILENIQSTWKVGVIANSGDNAVSLKVTRFEDLKVIIDHFEKYPLITQKLGDYKLFKQAFSVMENKEHLKENGIKELVRIKAKLNWGLTDELKKAFPENISKERSLINKNIPNFKWLAGFTSGEGHFAVNLIKSKSKLGVQVQLRFTITQHIKDKNLMNSLITYLGCGYIREFNKSEFSWLEFRVTKFSDINDKIIPVFQENTLIGVKLEDFEDWCKVAKLIEEKKHLTESGLDEIKKIKLNMNKGR

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (26-MER)
formula_weight	7943.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GGGTTTCCACTTATTCAAACTTTTAG

Entity 3 polymer

description	DNA (26-MER)
formula_weight	8028.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

CCTAAAAGTTTGAATAAGTGGAAACC

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	197

▶

6. Citations (1)

▶

length_a	39.306 Å
length_b	76.155 Å
length_c	167.817 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	2.402 Å
resolution_low	32.246 Å
r_factor	0.1991
r_work	0.1941
r_free	0.2435

fit	/app/data/saxs_computation/xy/9xy2/9xy2.fit
pddf	/app/data/pr_computation/xy/9xy2/9xy2.pr.out
profile	/app/data/saxs_computation/xy/9xy2/9xy2.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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)