5U2I

Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri

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	2016-10-12
Detector	MARMOSAIC 225 mm CCD
Wavelength(s)	0.97872
Spacegroup name	P 1 21 1
Unit cell lengths	67.900, 110.380, 68.140
Unit cell angles	90.00, 118.55, 90.00

Refinement procedure

Resolution	40.575 - 1.400
R-factor	0.141
Rwork	0.141
R-free	0.16890
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3vvt
RMSD bond length	0.010
RMSD bond angle	1.110
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MoRDa
Refinement software	PHENIX

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	40.592		1.440
High resolution limit [Å]	1.400	6.260	1.400
Rmerge	0.113	0.090	0.405
Number of reflections	172534
<I/σ(I)>	9.08	15.34	3.37
Completeness [%]	99.6	98.4	99.8
Redundancy	4.16
CC(1/2)	0.988	0.980	0.864

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	Rigaku Reagents MCSG1 screen g10: 0.1M Mg Formate, 15% PEG3350; NafoA.00438.a.B1.PS38003 at 17.9 mg/mL. Tray 283886 g10, puck fhx0-10; cryoprotected in 20% ethylene glycol