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10dc

H-Ras GTPase R68A bound to GppNHp

Method: X-RAY DIFFRACTION D_max: 48.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10dc
deposition_date	2026-01-13
title	H-Ras GTPase R68A bound to GppNHp
keywords	small GTPase, Ras GTPase, GTP analog, HYDROLASE, SIGNALING PROTEIN; HYDROLASE, 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	15.97 Å
rg_electron	14.64 Å
i0	7003920.00
molecular_weight	18305.0 kDa
excluded_volume	22475 Å³
envelope_volume	24716 Å³
shell_volume	14092 Å³
envelope_diameter	48.4 Å
shell_rg	20.73 Å
envelope_rg	14.87 Å
shape_rg	14.64 Å
total_rg	15.71 Å
total_atoms	1280
n_residues	162
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	48.8 Å
rg_real	15.83 Å
rg_real_error	0.24 Å
i0_real	7.0040e+06
i0_real_error	7.8230e+04
rg_reciprocal	15.84 Å
i0_reciprocal	7004000.0000
total_estimate	0.8985
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.0 Å
skewness	0.009
kurtosis	-0.503
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	1116000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	GTPase HRas
formula_weight	18789.1 kDa
ec_number	3.6.5.2
mutation	R68A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1406

MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMADQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
formula_weight	522.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	126

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6. Citations (1)

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length_a	69.896 Å
length_b	69.896 Å
length_c	33.321 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 41
int_tables_number	76
crystal_system	tetragonal

resolution	2.080 Å
resolution_low	23.300 Å
r_factor	0.1697
r_work	0.1646
r_free	0.2149

fit	/app/data/saxs_computation/0d/10dc/10dc.fit
pddf	/app/data/pr_computation/0d/10dc/10dc.pr.out
profile	/app/data/saxs_computation/0d/10dc/10dc.dat

H-Ras GTPase R68A bound to GppNHp

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