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9r2b

De novo-designed alpha-helical barrel

Method: X-RAY DIFFRACTION D_max: 84.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r2b
deposition_date	2025-04-29
last_revision	2026-05-06
title	De novo-designed alpha-helical barrel
keywords	de novo enzyme, DE NOVO PROTEIN; DE NOVO 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	27.30 Å
rg_electron	26.59 Å
i0	19185600.00
molecular_weight	36959.0 kDa
excluded_volume	48138 Å³
envelope_volume	63087 Å³
shell_volume	21132 Å³
envelope_diameter	89.2 Å
shell_rg	31.98 Å
envelope_rg	26.14 Å
shape_rg	26.56 Å
total_rg	27.42 Å
total_atoms	2570
n_residues	338
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	84.6 Å
rg_real	27.49 Å
rg_real_error	0.61 Å
i0_real	1.9190e+07
i0_real_error	2.6240e+05
rg_reciprocal	27.44 Å
i0_reciprocal	19180000.0000
total_estimate	0.8443
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.3 Å
skewness	0.397
kurtosis	-0.668
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	9178000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.773

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	de novo-designed alpha-helical barrel
formula_weight	22284.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	2785

ENLYFQGSHMTCEVVKKILYMAKKLVEKKKEVVKKIEKGQEDPATLLLEMLEEELKLAEKIAKLMLESGISEEVVKKILYMAKKLVEKKKEVVKKIEKGGTDPAELLLEMLEEELKLAEKIAKLMLESGISEEVVKKILKMAKKLVEKKKEVVKKIAKDRKNAAKLLLEMLEEELKLAEKIAKLMEEQCKGSGW

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 non-polymer

description	HEXAETHYLENE GLYCOL
formula_weight	282.3 kDa
src_method	syn
entity_count	2

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	191

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6. Citations (1)

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length_a	149.400 Å
length_b	33.270 Å
length_c	102.710 Å
angle_alpha	90.00 °
angle_beta	133.13 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.100 Å
resolution_low	37.280 Å
r_factor	0.2702
r_work	0.2665
r_free	0.3074

fit	/app/data/saxs_computation/r2/9r2b/9r2b.fit
pddf	/app/data/pr_computation/r2/9r2b/9r2b.pr.out
profile	/app/data/saxs_computation/r2/9r2b/9r2b.dat

De novo-designed alpha-helical barrel

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