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10wy

Rhodococcus hoagii DnaA DI in the P4(3)2(1)2 space group

Method: X-RAY DIFFRACTION D_max: 58.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10wy
deposition_date	2026-02-11
last_revision	2026-06-03
title	Rhodococcus hoagii DnaA DI in the P4(3)2(1)2 space group
keywords	Initiator, 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	18.09 Å
rg_electron	16.76 Å
i0	6905710.00
molecular_weight	19403.0 kDa
excluded_volume	24523 Å³
envelope_volume	28892 Å³
shell_volume	14908 Å³
envelope_diameter	60.3 Å
shell_rg	22.24 Å
envelope_rg	17.09 Å
shape_rg	16.73 Å
total_rg	17.85 Å
total_atoms	2775
n_residues	178
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	58.7 Å
rg_real	18.07 Å
rg_real_error	0.41 Å
i0_real	6.9060e+06
i0_real_error	8.3380e+04
rg_reciprocal	18.07 Å
i0_reciprocal	6906000.0000
total_estimate	0.6350
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.2 Å
skewness	0.354
kurtosis	-0.224
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	1696000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 0.999; Sysdev: 0.275; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Chromosomal replication initiator protein DnaA
formula_weight	14299.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3005

MGSSHHHHHHSSGLVPRGSHMNDDPNALANVWRDVVAELTSDASDSPKLTKAQKAWLALVRPLTYAQGFALLSVPSPLAQEAIERDLREPILRALNRHLGQKVEGLGVRIAAPSEDRGEDSGDAAPADETDR

Source

organism	Prescottella equi
ncbi_taxonomy_id	43767
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	144

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6. Citations (1)

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length_a	60.646 Å
length_b	60.646 Å
length_c	132.457 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	1.600 Å
resolution_low	44.730 Å
r_factor	0.1757
r_work	0.1745
r_free	0.1978

fit	/app/data/saxs_computation/0w/10wy/10wy.fit
pddf	/app/data/pr_computation/0w/10wy/10wy.pr.out
profile	/app/data/saxs_computation/0w/10wy/10wy.dat