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9v39

Crystal structure of de novo designed serotonin binder SROb2_30

Method: X-RAY DIFFRACTION D_max: 72.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v39
deposition_date	2025-05-21
last_revision	2026-05-27
title	Crystal structure of de novo designed serotonin binder SROb2_30
keywords	small molecule binding complex, 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	21.34 Å
rg_electron	20.78 Å
i0	8664830.00
molecular_weight	20591.0 kDa
excluded_volume	25184 Å³
envelope_volume	33519 Å³
shell_volume	14558 Å³
envelope_diameter	73.0 Å
shell_rg	25.56 Å
envelope_rg	20.31 Å
shape_rg	20.78 Å
total_rg	21.49 Å
total_atoms	1454
n_residues	212
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	72.2 Å
rg_real	21.44 Å
rg_real_error	0.60 Å
i0_real	8.6650e+06
i0_real_error	1.1460e+05
rg_reciprocal	21.42 Å
i0_reciprocal	8665000.0000
total_estimate	0.7716
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	18.1 Å
skewness	0.383
kurtosis	-0.493
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	1858000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.746; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.795; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	De novo designed serotonin binder SROb2_30, chain A
formula_weight	13383.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	1545

GKEAALKTIKEAIKKAKERGDEEVIEYLKELEKAVEAGNADEAVELLKKIQKIAIDRGDEELSNTVANIIGTGLKAGVLSEEAYEKLADAYVEEVVKKGTKTREEVQEEVERFKKEVLEN

Source

organism	Escherichia coli BL21(DE3)
ncbi_taxonomy_id	469008
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	SEROTONIN
formula_weight	176.2 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	91

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6. Citations (1)

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length_a	55.330 Å
length_b	42.760 Å
length_c	86.305 Å
angle_alpha	90.00 °
angle_beta	100.71 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.580 Å
resolution_low	27.240 Å
r_factor	0.3058
r_work	0.2980
r_free	0.3673

fit	/app/data/saxs_computation/v3/9v39/9v39.fit
pddf	/app/data/pr_computation/v3/9v39/9v39.pr.out
profile	/app/data/saxs_computation/v3/9v39/9v39.dat

Crystal structure of de novo designed serotonin binder SROb2_30

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