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9r2o

De novo designed N5 protein fold

Method: X-RAY DIFFRACTION D_max: 76.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r2o
deposition_date	2025-04-30
title	De novo designed N5 protein fold
keywords	dark fold, de novo, unnatural, 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	24.39 Å
rg_electron	23.16 Å
i0	25885900.00
molecular_weight	37117.0 kDa
excluded_volume	45759 Å³
envelope_volume	60962 Å³
shell_volume	22808 Å³
envelope_diameter	80.0 Å
shell_rg	29.07 Å
envelope_rg	23.61 Å
shape_rg	23.17 Å
total_rg	23.88 Å
total_atoms	2605
n_residues	307
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	76.8 Å
rg_real	24.37 Å
rg_real_error	0.43 Å
i0_real	2.5890e+07
i0_real_error	3.3460e+05
rg_reciprocal	24.37 Å
i0_reciprocal	25890000.0000
total_estimate	0.9066
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.0 Å
skewness	0.300
kurtosis	-0.398
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	2437000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	N5
formula_weight	20165.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2727

SREETRDDDGTRELRYKNPFDGSEITIRSPRSEDFERVSTEVLLLELLETIGLLLSREELEELIKLLQEEYPEWTPDQALQWLRDTTEKTIKEAAEQGWNKEQAFELLLSSVPEKIAEYLKKLKEERETDEERRKQTEEDREEWEEELRERGYTISRGGSGGSHHHHHH

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	11

Entity 3 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	122

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6. Citations (2)

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length_a	112.710 Å
length_b	38.250 Å
length_c	77.470 Å
angle_alpha	90.00 °
angle_beta	112.64 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.090 Å
resolution_low	52.830 Å
r_factor	0.2437
r_work	0.2422
r_free	0.2719

fit	/app/data/saxs_computation/r2/9r2o/9r2o.fit
pddf	/app/data/pr_computation/r2/9r2o/9r2o.pr.out
profile	/app/data/saxs_computation/r2/9r2o/9r2o.dat

De novo designed N5 protein fold

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