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9y1c

WT human DNA polymerase beta, Ternary complex dG:dCmpCpp

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y1c
deposition_date	2025-08-29
title	WT human DNA polymerase beta, Ternary complex dG:dCmpCpp
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	22.92 Å
rg_electron	22.25 Å
i0	48114300.00
molecular_weight	47243.0 kDa
excluded_volume	56313 Å³
envelope_volume	71235 Å³
shell_volume	26155 Å³
envelope_diameter	76.9 Å
shell_rg	29.56 Å
envelope_rg	22.43 Å
shape_rg	22.25 Å
total_rg	23.04 Å
total_atoms	3279
n_residues	357
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	73.2 Å
rg_real	22.78 Å
rg_real_error	0.43 Å
i0_real	4.8110e+07
i0_real_error	6.5060e+05
rg_reciprocal	22.82 Å
i0_reciprocal	48120000.0000
total_estimate	0.8937
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.4 Å
skewness	0.141
kurtosis	-0.421
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	5626000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

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	3894

MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Template strand
formula_weight	4869.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

CCGACGGCGCATCAGC

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	2

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
formula_weight	465.2 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	571

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6. Citations (1)

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length_a	50.690 Å
length_b	79.692 Å
length_c	55.506 Å
angle_alpha	90.00 °
angle_beta	107.44 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.900 Å
resolution_low	20.670 Å
r_factor	0.1586
r_work	0.1544
r_free	0.1975

fit	/app/data/saxs_computation/y1/9y1c/9y1c.fit
pddf	/app/data/pr_computation/y1/9y1c/9y1c.pr.out
profile	/app/data/saxs_computation/y1/9y1c/9y1c.dat

WT human DNA polymerase beta, Ternary complex dG:dCmpCpp

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 (9)

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 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)