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9y15

WT human DNA polymerase beta, Binary complex templating dA

Method: X-RAY DIFFRACTION D_max: 70.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y15
deposition_date	2025-08-29
title	WT human DNA polymerase beta, Binary complex templating dA
keywords	polymerase, REPLICATION, HYDROLASE-DNA complex; REPLICATION, HYDROLASE/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	23.51 Å
rg_electron	22.89 Å
i0	45320300.00
molecular_weight	46055.0 kDa
excluded_volume	55043 Å³
envelope_volume	71486 Å³
shell_volume	25936 Å³
envelope_diameter	72.8 Å
shell_rg	29.83 Å
envelope_rg	22.69 Å
shape_rg	22.88 Å
total_rg	23.67 Å
total_atoms	3202
n_residues	354
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	70.5 Å
rg_real	23.34 Å
rg_real_error	0.34 Å
i0_real	4.5320e+07
i0_real_error	5.1240e+05
rg_reciprocal	23.38 Å
i0_reciprocal	45320000.0000
total_estimate	0.9102
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	31.5 Å
skewness	0.070
kurtosis	-0.495
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	4171000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	DNA polymerase beta
formula_weight	38241.7 kDa
ec_number	2.7.7.7,4.2.99.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3832

MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Template strand
formula_weight	4853.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

CCGACAGCGCATCAGC

Entity 3 polymer

description	Primer strand
formula_weight	3061.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

GCTGATGCGC

Entity 4 polymer

description	Downstream
formula_weight	1536.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GTCGG

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	582

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6. Citations (1)

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length_a	54.333 Å
length_b	78.595 Å
length_c	54.771 Å
angle_alpha	90.00 °
angle_beta	104.62 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.850 Å
resolution_low	23.450 Å
r_factor	0.1721
r_work	0.1676
r_free	0.2121

fit	/app/data/saxs_computation/y1/9y15/9y15.fit
pddf	/app/data/pr_computation/y1/9y15/9y15.pr.out
profile	/app/data/saxs_computation/y1/9y15/9y15.dat

WT human DNA polymerase beta, Binary complex templating dA

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 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)