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9que

Structure of human MTH1 in complex with 8DG by continuous serial electron diffraction (SerialED)

Method: ELECTRON CRYSTALLOGRAPHY D_max: 76.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9que
deposition_date	2025-04-10
last_revision	2026-04-22
title	Structure of human MTH1 in complex with 8DG by continuous serial electron diffraction (SerialED)
keywords	serial electron diffraction, SerialED, 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	24.19 Å
rg_electron	23.19 Å
i0	25495800.00
molecular_weight	37356.0 kDa
excluded_volume	46172 Å³
envelope_volume	55412 Å³
shell_volume	20912 Å³
envelope_diameter	77.7 Å
shell_rg	28.64 Å
envelope_rg	23.11 Å
shape_rg	23.14 Å
total_rg	24.03 Å
total_atoms	5109
n_residues	311
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	76.9 Å
rg_real	24.31 Å
rg_real_error	0.52 Å
i0_real	2.5500e+07
i0_real_error	3.3970e+05
rg_reciprocal	24.29 Å
i0_reciprocal	25500000.0000
total_estimate	0.8741
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.0 Å
skewness	0.413
kurtosis	-0.588
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	6613000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Oxidized purine nucleoside triphosphate hydrolase
formula_weight	18253.7 kDa
ec_number	3.6.1.56,3.6.1.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5299

GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	141

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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	1.660 Å
resolution_low	25.730 Å
r_factor	0.2074
r_work	0.2051
r_free	0.2528

resolution	1.66 Å
resolution_method	—
num_particles	—

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

Structure of human MTH1 in complex with 8DG by continuous serial electron diffraction (SerialED)

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