9VSB

Small molecule LC-YD03 targeting YTHDC1

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL18U1
Synchrotron site	SSRF
Beamline	BL18U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-05-09
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.97853
Spacegroup name	P 1 21 1
Unit cell lengths	39.448, 103.341, 41.452
Unit cell angles	90.00, 105.59, 90.00

Refinement procedure

Resolution	30.720 - 1.800
R-factor	0.2448
Rwork	0.243
R-free	0.27360
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.016
RMSD bond angle	1.315
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (v1.20)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	51.670	1.900
High resolution limit [Å]	1.800	1.800
Rmerge	0.114	0.552
Rmeas	0.129	0.619
Rpim	0.058	0.274
Total number of observations	129778	19434
Number of reflections	28723	4147
<I/σ(I)>	8.6	2.7
Completeness [%]	97.7
Redundancy	4.5	4.7
CC(1/2)	0.996	0.749

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	EVAPORATION		289.15	0.1M Bis-Tris PH = 7.5 20% PEG3350 0.2M Ammonium sulfate