SAXSdb — 9uoj

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1. Structure Basics

entry_id	9uoj
deposition_date	2025-04-25
last_revision	2026-04-29
title	WDR5 bound with P3
keywords	WDR5, STRUCTURAL GENOMICS; STRUCTURAL GENOMICS
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	18.58 Å
rg_electron	17.73 Å
i0	35308500.00
molecular_weight	31302.0 kDa
excluded_volume	30431 Å³
envelope_volume	45522 Å³
shell_volume	20648 Å³
envelope_diameter	56.5 Å
shell_rg	24.79 Å
envelope_rg	17.91 Å
shape_rg	17.71 Å
total_rg	18.41 Å
total_atoms	2373
n_residues	304
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	55.6 Å
rg_real	18.42 Å
rg_real_error	0.18 Å
i0_real	3.5310e+07
i0_real_error	3.6180e+05
rg_reciprocal	18.45 Å
i0_reciprocal	35310000.0000
total_estimate	0.9054
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.063
kurtosis	-0.533
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	12420000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	WD repeat-containing protein 5
formula_weight	34478.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2562

SSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;~{N}-[5-[2-fluoranyl-5-[4-[[4-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,1,3-benzoxadiazol-7-yl]amino]butylcarbamoyl]phenyl]-2-[(3~{R},5~{S})-3,4,5-trimethylpiperazin-1-yl]phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1~{H}-pyridine-3-carboxamide ;
formula_weight	780.7 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	178

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6. Citations (1)

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length_a	81.483 Å
length_b	86.586 Å
length_c	41.533 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.820 Å
resolution_low	41.530 Å
r_factor	0.2123
r_work	0.2099
r_free	0.2537

fit	/app/data/saxs_computation/uo/9uoj/9uoj.fit
pddf	/app/data/pr_computation/uo/9uoj/9uoj.pr.out
profile	/app/data/saxs_computation/uo/9uoj/9uoj.dat

WDR5 bound with P3

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