← Back to search

9rbe

Crystal structure of a computationally designed protein bound to a gold cofactor (TRP_F43W.[sulfaNHC)Au])

Method: X-RAY DIFFRACTION D_max: 54.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rbe
deposition_date	2025-05-22
last_revision	2026-06-03
title	Crystal structure of a computationally designed protein bound to a gold cofactor (TRP_F43W.[sulfaNHC)Au])
keywords	DE NOVO PROTEIN; DE NOVO PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	17.99 Å
rg_electron	17.17 Å
i0	16423300.00
molecular_weight	20961.0 kDa
excluded_volume	20468 Å³
envelope_volume	33186 Å³
shell_volume	16138 Å³
envelope_diameter	54.7 Å
shell_rg	23.17 Å
envelope_rg	17.39 Å
shape_rg	17.22 Å
total_rg	17.83 Å
total_atoms	1587
n_residues	208
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

▼

3. P(r) Analysis (GNOM)

dmax	54.4 Å
rg_real	17.88 Å
rg_real_error	0.31 Å
i0_real	1.6420e+07
i0_real_error	1.9960e+05
rg_reciprocal	17.90 Å
i0_reciprocal	16420000.0000
total_estimate	0.8278
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	19.1 Å
skewness	0.170
kurtosis	-0.532
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	6854000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	[(sulfaNHC)Au].TRP_F43W
formula_weight	22619.0 kDa
mutation	F43W
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1725

GGGSGVSLEQALLILSVAALLGTTVEEAVKRALWLKTKLGVSLEQAAWILSVAAYLGTTVEEAVKRALKLKTKLGVSLEQALLILFAAAALGTTVEEAVKRALKLKTKLGVSLEQALLILFTAAELGTTVEEAVKRALKLKTKLGVSLEQAQAILVVAAELGTTVEEAVYRALKLKTKLGVSLEQALLILEVAAKLGTTVEEAVKRALKLKTKLG

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;[(3~{a}~{R},8~{a}~{R})-6,6-bis(oxidanylidene)-1,3-bis(2,4,6-trimethylphenyl)-3~{a},4,5,7,8,8~{a}-hexahydro-2~{H}-imidazo[4,5-d][1,2,7]thiadiazepin-2-yl]-chloranyl-gold ;
formula_weight	660.0 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	65

▶

6. Citations (1)

▶

length_a	35.941 Å
length_b	60.023 Å
length_c	53.756 Å
angle_alpha	90.00 °
angle_beta	92.38 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	40.020 Å
r_factor	—
r_work	0.2248
r_free	0.2862

fit	/app/data/saxs_computation/rb/9rbe/9rbe.fit
pddf	/app/data/pr_computation/rb/9rbe/9rbe.pr.out
profile	/app/data/saxs_computation/rb/9rbe/9rbe.dat

Crystal structure of a computationally designed protein bound to a gold cofactor (TRP_F43W.[sulfaNHC)Au])

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