SAXSdb — 9u6a

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1. Structure Basics

entry_id	9u6a
deposition_date	2025-03-22
title	Tubulin-DARPin D1 in complex with a flavone
keywords	Tubulin, CELL CYCLE; CELL CYCLE
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	33.97 Å
rg_electron	33.98 Å
i0	387903000.00
molecular_weight	105090.0 kDa
excluded_volume	100920 Å³
envelope_volume	167910 Å³
shell_volume	42733 Å³
envelope_diameter	133.9 Å
shell_rg	39.02 Å
envelope_rg	34.52 Å
shape_rg	33.98 Å
total_rg	34.23 Å
total_atoms	7933
n_residues	1015
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	123.6 Å
rg_real	34.24 Å
rg_real_error	1.04 Å
i0_real	3.8790e+08
i0_real_error	5.7310e+06
rg_reciprocal	34.07 Å
i0_reciprocal	387800000.0000
total_estimate	0.8010
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.2 Å
skewness	0.638
kurtosis	0.034
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	51000000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.607; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.684; Smooth: 0.903

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Tubulin alpha-1B chain
formula_weight	50204.4 kDa
ec_number	3.6.5.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8452

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 polymer

description	Tubulin beta chain
formula_weight	48299.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD

Entity 3 polymer

description	Designed Ankyrin Repeat Protein (DARPIN) D1
formula_weight	18068.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 4 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	3-methoxy-2-(4-methoxy-3-oxidanyl-phenyl)-5,7-bis(oxidanyl)chromen-4-one
formula_weight	330.3 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	511

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6. Citations (1)

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length_a	73.600 Å
length_b	91.080 Å
length_c	83.170 Å
angle_alpha	90.00 °
angle_beta	97.28 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.920 Å
resolution_low	35.070 Å
r_factor	0.1841
r_work	0.1831
r_free	0.2235

fit	/app/data/saxs_computation/u6/9u6a/9u6a.fit
pddf	/app/data/pr_computation/u6/9u6a/9u6a.pr.out
profile	/app/data/saxs_computation/u6/9u6a/9u6a.dat

Tubulin-DARPin D1 in complex with a flavone

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

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)