9MB3

Crystal structure of YTHDC1 in complex with YL-5092

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL19U1
Synchrotron site	SSRF
Beamline	BL19U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-11-17
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97853
Spacegroup name	P 2 21 21
Unit cell lengths	73.152, 74.405, 75.539
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	37.770 - 1.600
R-factor	0.2008
Rwork	0.199
R-free	0.22560
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4r3i
RMSD bond length	0.006
RMSD bond angle	0.854
Data reduction software	HKL-3000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.290
High resolution limit [Å]	1.600	6.100	2.250
Rmerge	0.072	0.041	0.543
Rmeas	0.085	0.048	0.638
Rpim	0.044	0.025	0.332
Number of reflections	71126	3593	3543
<I/σ(I)>	6.5
Completeness [%]	98.1	99.4	97.5
Redundancy	3.5	3.4	3.6
CC(1/2)		0.994	0.771

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	25% PEG 3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5