9SZP

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

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-06-20
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.05965
Spacegroup name	C 2 2 21
Unit cell lengths	74.570, 115.469, 39.951
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	34.200 - 1.580
R-factor	0.2008
Rwork	0.199
R-free	0.23100
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.860
Data reduction software	XDS
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	63.000	1.630
High resolution limit [Å]	1.500	1.500
Number of reflections	26232	1011
<I/σ(I)>	7.7
Completeness [%]	99.7
Redundancy	20
CC(1/2)	0.996	0.477

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		295	20% PEG 3350, 200 mM KNO3