6MN8

Crystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofuginone and nucleotide

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2018-07-05
Detector	MARMOSAIC 300 mm CCD
Wavelength(s)	0.97872
Spacegroup name	H 3 2
Unit cell lengths	159.720, 159.720, 143.720
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	42.276 - 2.350
R-factor	0.1438
Rwork	0.142
R-free	0.17950
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4hvc
RMSD bond length	0.007
RMSD bond angle	0.877
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MoRDa
Refinement software	PHENIX ((1.14_3260))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	42.276	42.276	2.410
High resolution limit [Å]	2.350	10.510	2.350
Rmerge	0.085	0.040	0.598
Rmeas	0.090	0.043	0.632
Total number of observations	278849
Number of reflections	29419	364	2166
<I/σ(I)>	19.16	45.03	3.97
Completeness [%]	100.0	97.3	100
Redundancy	9.479	8.148	9.548
CC(1/2)	0.999	0.999	0.907

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	OnvoA.17194.a.B5.PW38185 at 17 mg/ml was incubated with 2 mM halofuginone, AMPPNP, and MgCl2, then was mixed 1:1 Morpheus(h12): 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.02 M each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, 0.1 M bicine/Trizma base, pH=8.5. Tray: 389737h12, puck: lte2-7