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9t3d

RACB with GPPNHP bound

Method: X-RAY DIFFRACTION D_max: 58.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t3d
deposition_date	2025-10-27
title	RACB with GPPNHP bound
keywords	RACB, Hordeum vulgare, GPPNHP, PLANT PROTEIN; PLANT 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	17.39 Å
rg_electron	16.21 Å
i0	7963870.00
molecular_weight	20956.0 kDa
excluded_volume	26397 Å³
envelope_volume	30355 Å³
shell_volume	15683 Å³
envelope_diameter	60.3 Å
shell_rg	22.38 Å
envelope_rg	16.80 Å
shape_rg	16.21 Å
total_rg	17.32 Å
total_atoms	1471
n_residues	184
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	58.3 Å
rg_real	17.31 Å
rg_real_error	0.34 Å
i0_real	7.9640e+06
i0_real_error	9.9610e+04
rg_reciprocal	17.32 Å
i0_reciprocal	7964000.0000
total_estimate	0.7948
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	22.2 Å
skewness	0.231
kurtosis	-0.241
angular_range	— – 0.4600 Å⁻¹
current_alpha	0.0000
highest_alpha	1669000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	RACB protein
formula_weight	21809.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1969

GSGMSASRFIKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVSKKWIPELKHYAPGVPIILVGTKLDLRDDKQFFVDHPGAVPITTAQGEELKKLIGAPYYIECSSKTQLNVKGVFDAAIKVVLQPPKAKKKKKAQRGACSIL

Source

organism	Hordeum vulgare
ncbi_taxonomy_id	4513
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	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	FLUORIDE ION
formula_weight	19.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	214

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6. Citations (1)

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length_a	85.710 Å
length_b	66.700 Å
length_c	37.100 Å
angle_alpha	90.00 °
angle_beta	93.59 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.330 Å
resolution_low	42.810 Å
r_factor	0.1177
r_work	0.1164
r_free	0.1395

fit	/app/data/saxs_computation/t3/9t3d/9t3d.fit
pddf	/app/data/pr_computation/t3/9t3d/9t3d.pr.out
profile	/app/data/saxs_computation/t3/9t3d/9t3d.dat