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9quk

Structure of human MTH1 in complex with 8DG by MicroED using low electron fluence

Method: ELECTRON CRYSTALLOGRAPHY D_max: 77.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9quk
deposition_date	2025-04-10
last_revision	2026-04-22
title	Structure of human MTH1 in complex with 8DG by MicroED using low electron fluence
keywords	serial electron diffraction, SerialED, MicroED, MTH1, 8DG, Hydrolase; HYDROLASE
method	ELECTRON CRYSTALLOGRAPHY

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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	24.33 Å
rg_electron	23.29 Å
i0	24995000.00
molecular_weight	37096.0 kDa
excluded_volume	45821 Å³
envelope_volume	55036 Å³
shell_volume	20619 Å³
envelope_diameter	78.5 Å
shell_rg	29.04 Å
envelope_rg	23.23 Å
shape_rg	23.23 Å
total_rg	24.16 Å
total_atoms	5067
n_residues	309
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	77.8 Å
rg_real	24.47 Å
rg_real_error	0.48 Å
i0_real	2.5000e+07
i0_real_error	3.5280e+05
rg_reciprocal	24.44 Å
i0_reciprocal	24990000.0000
total_estimate	0.8680
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.406
kurtosis	-0.617
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	5985000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.864; Smooth: 0.973

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	7,8-dihydro-8-oxoguanine triphosphatase
formula_weight	18253.7 kDa
ec_number	3.6.1.55,3.6.1.56
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5094

GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	11

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6. Citations (1)

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length_a	59.340 Å
length_b	67.550 Å
length_c	80.110 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.860 Å
resolution_low	29.670 Å
r_factor	0.2341
r_work	0.2314
r_free	0.2824

resolution	2.86 Å
resolution_method	—
num_particles	—

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

Structure of human MTH1 in complex with 8DG by MicroED using low electron fluence

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