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9quc

Metal-free de novo protein scaffold TFD-EH

Method: X-RAY DIFFRACTION D_max: 55.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9quc
deposition_date	2025-04-10
title	Metal-free de novo protein scaffold TFD-EH
keywords	TIM barrel, Enzyme Engineering, Metal Coordination, Conformational Dynamics, 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	17.83 Å
rg_electron	16.88 Å
i0	6847420.00
molecular_weight	19378.0 kDa
excluded_volume	24514 Å³
envelope_volume	29506 Å³
shell_volume	14897 Å³
envelope_diameter	54.2 Å
shell_rg	22.54 Å
envelope_rg	17.18 Å
shape_rg	16.84 Å
total_rg	17.98 Å
total_atoms	1357
n_residues	171
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	55.3 Å
rg_real	17.75 Å
rg_real_error	0.35 Å
i0_real	6.8470e+06
i0_real_error	7.7480e+04
rg_reciprocal	17.76 Å
i0_reciprocal	6847000.0000
total_estimate	0.8258
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.4 Å
skewness	0.193
kurtosis	-0.546
angular_range	— – 0.4450 Å⁻¹
current_alpha	0.0000
highest_alpha	2008000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 0.996; 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 (4)

Entity 1 polymer

description	TFD-EH
formula_weight	18916.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1514

GAMGDILIVWAKDVDEMLKQVEILRRLGAKQIAVESSDWRILQEALKKGGDILIVNGGGMTITFRGDDLEALLKAAIEMIKQALKFGATITLSLDGNDLNINITGVPEQVRKELAKEAERLAKEFGITVTRTGGGDVDEMLKQVEILRRLGAKQIAVHSDDWRILQEALKKG

Source

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

Entity 2 non-polymer

description	CITRIC ACID
formula_weight	192.1 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	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	157

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6. Citations (1)

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length_a	78.670 Å
length_b	78.670 Å
length_c	66.260 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	1.600 Å
resolution_low	30.000 Å
r_factor	0.1581
r_work	0.1568
r_free	0.1839

fit	/app/data/saxs_computation/qu/9quc/9quc.fit
pddf	/app/data/pr_computation/qu/9quc/9quc.pr.out
profile	/app/data/saxs_computation/qu/9quc/9quc.dat

Metal-free de novo protein scaffold TFD-EH

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