SAXSdb — 9rd5

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1. Structure Basics

entry_id	9rd5
deposition_date	2025-06-01
title	Phi3T SroF bound to DNA
keywords	Recombinase, arbitrium repressor, YopR, 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	25.38 Å
rg_electron	24.38 Å
i0	64999600.00
molecular_weight	53230.0 kDa
excluded_volume	62406 Å³
envelope_volume	79213 Å³
shell_volume	27549 Å³
envelope_diameter	89.3 Å
shell_rg	31.04 Å
envelope_rg	24.44 Å
shape_rg	24.33 Å
total_rg	25.14 Å
total_atoms	3686
n_residues	369
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	86.3 Å
rg_real	25.38 Å
rg_real_error	0.70 Å
i0_real	6.5000e+07
i0_real_error	8.5030e+05
rg_reciprocal	25.38 Å
i0_reciprocal	65000000.0000
total_estimate	0.8760
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.8 Å
skewness	0.364
kurtosis	-0.295
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	6987000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DNA (26-MER)
formula_weight	8019.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	3809

CATTAAGAATAAAAATAAAATTACTG

Entity 2 polymer

description	DNA (26-MER)
formula_weight	7947.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

CAGTAATTTTATTTTTATTCTTAATG

Entity 3 polymer

description	Core-binding (CB) domain-containing protein
formula_weight	38304.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

GSMSELYNAEIKEKFLERYESEATKELYRLKLRDFSFTERILDKDIFNFSLEELRTLFFDLDSKSLESLRGARAVIGQYTTWAMEHGLANSNINKVYEIKDEDLKQFIDKNKKTLFTNKEVEEYVSYLFNNQDKAMVQAVYEGIDGYQHSELINLTINDLLDDNKVRLQDDKHGERIIEVSEKCHELLRLAYEQNTYHLNNGSASGKLRFANLVRNEHIFRLKYKSPDQSMQADKFLVHRSFKTFQKILEEPYFTPKNLANSGKLNMAYKIYKKNKELTVPDYKKITAQYGFLNENAKFASQSLRKVVNMENIEKYCIQSEKIAD

Source

organism	Bacillus phage phi3T
ncbi_taxonomy_id	10736
host_organism	Escherichia coli

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	121

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6. Citations (1)

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length_a	75.182 Å
length_b	115.618 Å
length_c	154.372 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	orthorhombic

resolution	2.500 Å
resolution_low	58.350 Å
r_factor	0.2094
r_work	0.2071
r_free	0.2529

fit	/app/data/saxs_computation/rd/9rd5/9rd5.fit
pddf	/app/data/pr_computation/rd/9rd5/9rd5.pr.out
profile	/app/data/saxs_computation/rd/9rd5/9rd5.dat

Phi3T SroF bound to DNA

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)