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9x56

Crystal structure of RhoGDI2 in complex with Compound 2542

Method: X-RAY DIFFRACTION D_max: 60.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x56
deposition_date	2025-10-12
title	Crystal structure of RhoGDI2 in complex with Compound 2542
keywords	Inhibitor, Complex, Rho GDP-dissociation inhibitor 2, SIGNALING PROTEIN; SIGNALING 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	16.41 Å
rg_electron	15.39 Å
i0	8877640.00
molecular_weight	14950.0 kDa
excluded_volume	14565 Å³
envelope_volume	23063 Å³
shell_volume	13042 Å³
envelope_diameter	56.9 Å
shell_rg	20.94 Å
envelope_rg	15.80 Å
shape_rg	15.34 Å
total_rg	16.28 Å
total_atoms	1134
n_residues	137
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	60.5 Å
rg_real	16.40 Å
rg_real_error	0.43 Å
i0_real	8.8780e+06
i0_real_error	1.1440e+05
rg_reciprocal	16.40 Å
i0_reciprocal	8878000.0000
total_estimate	0.6661
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	19.4 Å
skewness	0.390
kurtosis	-0.128
angular_range	— – 0.4850 Å⁻¹
current_alpha	0.0000
highest_alpha	1759000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 0.287; Positv: 1.000; Valcen: 0.933; Smooth: 1.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Rho GDP-dissociation inhibitor 2
formula_weight	16158.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1313

DPKAPNVVVTRLTLVCESAPGPITMDLTGDLEALKKETIVLKEGSEYRVKIHFKVNRDIVSGLKYVQHTYRTGVKVDKATFMVGSYGPRPEEYEFLTPVEEAPKGMLARGTYHNKSFFTDDDKQDHLSWEWNLSIKKEWTE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	(~{R})-[4-(2-fluorophenyl)phenyl]-(1,3-thiazol-2-yl)methanamine
formula_weight	284.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	179

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6. Citations (1)

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length_a	55.176 Å
length_b	55.176 Å
length_c	96.006 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.700 Å
resolution_low	27.680 Å
r_factor	0.1759
r_work	0.1739
r_free	0.2156

fit	/app/data/saxs_computation/x5/9x56/9x56.fit
pddf	/app/data/pr_computation/x5/9x56/9x56.pr.out
profile	/app/data/saxs_computation/x5/9x56/9x56.dat