5TRW

Crystal structure of Pyridoxamine kinase PDXY from Burkholderia xenovorans

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	2016-10-06
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 41 21 2
Unit cell lengths	58.870, 58.870, 175.770
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	43.942 - 1.600
R-factor	0.1524
Rwork	0.151
R-free	0.17920
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1vi9
RMSD bond length	0.008
RMSD bond angle	0.933
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MOLREP
Refinement software	PHENIX

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000		1.640
High resolution limit [Å]	1.600	7.160	1.600
Rmerge	0.075	0.038	0.559
Number of reflections	41948
<I/σ(I)>	18.7	37.95	3.98
Completeness [%]	100.0	98.5	100
Redundancy	9.51
CC(1/2)	0.999	0.998	0.912

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	Microlytic MCSG1 screen H7: 30% PEG 3000, 100mM CHES pH 9.5; BuxeA.00129.a.B1.PS37942 at 14.1mg/ml + 3mM MgCl2 + 3mM AMPPNP (not visible); cryo: 20% EG; tray 274724a2, puck JUS9-5