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9t1d

Cryo-EM reconstruction of undecorated GDP microtubule

Method: ELECTRON MICROSCOPY D_max: 98.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t1d
deposition_date	2025-10-21
title	Cryo-EM reconstruction of undecorated GDP microtubule
keywords	Microtubule. Tubulin dimer., STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

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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	29.72 Å
rg_electron	29.08 Å
i0	153640000.00
molecular_weight	96114.0 kDa
excluded_volume	119050 Å³
envelope_volume	141450 Å³
shell_volume	40030 Å³
envelope_diameter	106.3 Å
shell_rg	36.99 Å
envelope_rg	29.42 Å
shape_rg	29.09 Å
total_rg	29.68 Å
total_atoms	6746
n_residues	852
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	98.7 Å
rg_real	29.74 Å
rg_real_error	0.62 Å
i0_real	1.5360e+08
i0_real_error	2.1690e+06
rg_reciprocal	29.74 Å
i0_reciprocal	153600000.0000
total_estimate	0.6558
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	33.5 Å
skewness	0.425
kurtosis	-0.260
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	51410000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 0.050; Positv: 1.000; Valcen: 0.994; Smooth: 0.922

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Detyrosinated tubulin alpha-1A chain
formula_weight	48784.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6746

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS

Entity 2 polymer

description	Tubulin beta chain
formula_weight	48113.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDAT

Entity 3 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	6499207

fit	/app/data/saxs_computation/t1/9t1d/9t1d.fit
pddf	/app/data/pr_computation/t1/9t1d/9t1d.pr.out
profile	/app/data/saxs_computation/t1/9t1d/9t1d.dat

Cryo-EM reconstruction of undecorated GDP microtubule

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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)