20XT

Crystal structure of human ThrRS complexing with obafluorin derived inhibitor OB-D4

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	2025-03-20
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.979460
Spacegroup name	P 41 21 2
Unit cell lengths	73.422, 73.422, 356.353
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.840 - 3.500
R-factor	0.2185
Rwork	0.212
R-free	0.27680
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.569
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.840	3.830
High resolution limit [Å]	3.500	3.500
Rmerge	0.195	0.409
Number of reflections	13254	3045
<I/σ(I)>	20.4
Completeness [%]	100.0
Redundancy	23.7
CC(1/2)	0.997	0.983

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291.15	0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 0.045M imidazole, 0.055M MES monohydrate acid pH 6.5, 20% v/v glycol, 10% w/v PEG 8000