Crystal structure of the human YTHDC2 YTH domain in complex with m6A DNA

entry_id	9szp
deposition_date	2025-10-15
last_revision	2026-04-01
title	Crystal structure of the human YTHDC2 YTH domain in complex with m6A DNA
keywords	YTHDC2, DNA, m6A, RNA BINDING PROTEIN; RNA BINDING PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	15.54 Å
rg_electron	14.26 Å
i0	6442260.00
molecular_weight	17378.0 kDa
excluded_volume	21296 ų
envelope_volume	23602 ų
shell_volume	13730 ų
envelope_diameter	45.3 Å
shell_rg	20.43 Å
envelope_rg	14.56 Å
shape_rg	14.24 Å
total_rg	15.42 Å
total_atoms	1225
n_residues	141
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	47.5 Å
rg_real	15.42 Å
rg_real_error	0.23 Å
i0_real	6.4420e+06
i0_real_error	6.5300e+04
rg_reciprocal	15.43 Å
i0_reciprocal	6442000.0000
total_estimate	0.8976
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.0 Å
skewness	0.069
kurtosis	-0.428
angular_range	— – 0.5000 Å−1
current_alpha	0.0000
highest_alpha	1559000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.987

Unit Cell

length_a	74.570 Å
length_b	115.469 Å
length_c	39.951 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

Symmetry

space_group	C 2 2 21
int_tables_number	20
crystal_system	orthorhombic

Refinement

resolution	1.580 Å
resolution_low	34.200 Å
r_factor	0.2008
r_work	0.1993
r_free	0.2310

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/sz/9szp/pr_distribution.json
• pr_output /app/data/pr_computation/sz/9szp/9szp.pr.out
• pr_plot /app/data/visualization/pr_computation/sz/9szp/9szp_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/sz/9szp/9szp.dat
• saxs_fit /app/data/saxs_computation/sz/9szp/9szp.fit
• saxs_log /app/data/saxs_computation/sz/9szp/9szp.log
• saxs_plot /app/data/visualization/saxs_computation/sz/9szp/9szp_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/sz/9szp/9szp.fit
pddf	/app/data/pr_computation/sz/9szp/9szp.pr.out
profile	/app/data/saxs_computation/sz/9szp/9szp.dat