3P0H

Leishmania major Tyrosyl-tRNA synthetase in complex with fisetin, cubic crystal form

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL9-2
Synchrotron site	SSRL
Beamline	BL9-2
Temperature [K]	100
Detector technology	CCD
Collection date	2010-03-19
Detector	MARMOSAIC 325 mm CCD
Wavelength(s)	0.97931
Spacegroup name	I 2 3
Unit cell lengths	240.240, 240.240, 240.240
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.110 - 3.000
R-factor	0.2355
Rwork	0.234
R-free	0.27270
Structure solution method	MOLECULAR REPLACEMENT, SAD
Starting model (for MR)	Initial partial MR solution with PDB entry 2j5b then determined experimental phases and heavy atom positions by SAD. Also used PDB entries 2cya and 2cyc to aid in model completion.
RMSD bond length	0.006
RMSD bond angle	0.898
Data reduction software	MOSFLM
Data scaling software	SCALA (CCP4_3.3.9)
Phasing software	RESOLVE (2.13)
Refinement software	REFMAC (refmac_5.5.0110)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	47.110	47.110	3.160
High resolution limit [Å]	3.000	9.490	3.000
Rmerge	0.155	0.016	0.016
Total number of observations		21828	70153
Number of reflections	46076
<I/σ(I)>	14.0489
Completeness [%]	100.0	99.09	99.84
Redundancy	13.81	14.32	10.48

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 5 mM fisetin) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, and 4% w/v acetone); cryoprotected by addition of 30% PEG 3350, 10% MSGPP buffer, 10% ethylene glycol, and 0.1 M tri-sodium citrate pH 5.5 directly to drop prior to mounting and freezing crystals in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 277K