CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM

Method: X-RAY DIFFRACTION D_max: 89.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bpd
deposition_date	1994-04-12
title	CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM
keywords	NUCLEOTIDYLTRANSFERASE; NUCLEOTIDYLTRANSFERASE
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	27.84 Å
rg_electron	27.87 Å
i0	22247300.00
molecular_weight	35967.0 kDa
excluded_volume	44844 Å³
envelope_volume	63263 Å³
shell_volume	20115 Å³
envelope_diameter	95.0 Å
shell_rg	33.21 Å
envelope_rg	27.34 Å
shape_rg	27.88 Å
total_rg	28.43 Å
total_atoms	2533
n_residues	324
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	89.8 Å
rg_real	28.04 Å
rg_real_error	0.68 Å
i0_real	2.2250e+07
i0_real_error	3.2100e+05
rg_reciprocal	27.98 Å
i0_reciprocal	22250000.0000
total_estimate	0.8715
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.6 Å
skewness	0.347
kurtosis	-0.679
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	2371000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.736; Smooth: 0.888

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (3)

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length_a	39.499 Å
length_b	68.166 Å
length_c	75.280 Å
angle_alpha	90.00 °
angle_beta	91.68 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	3.600 Å
resolution_low	20.000 Å
r_factor	0.1930
r_work	—
r_free	—

description	DNA POLYMERASE BETA
formula_weight	38388.8 kDa
ec_number	2.7.7.7
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2533

CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (3)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

fit	/app/data/saxs_computation/bp/1bpd/1bpd.fit
pddf	/app/data/pr_computation/bp/1bpd/1bpd.pr.out
profile	/app/data/saxs_computation/bp/1bpd/1bpd.dat