6AY1

Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori

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	2017-08-18
Detector	RAYONIX MX-300
Wavelength(s)	0.97982
Spacegroup name	P 21 21 21
Unit cell lengths	63.190, 93.400, 208.490
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	45.571 - 2.050
R-factor	0.2073
Rwork	0.206
R-free	0.24080
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4hr2
RMSD bond length	0.007
RMSD bond angle	0.823
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]	45.571	45.571	2.100
High resolution limit [Å]	2.050	9.170	2.050
Rmerge	0.065	0.038	0.517
Rmeas	0.072	0.042	0.565
Number of reflections	78186	978	5703
<I/σ(I)>	14.61	30.15	3.25
Completeness [%]	99.8	97.5	100
Redundancy	5.926	5.162	6.169
CC(1/2)	0.998	0.997	0.938

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	24 mg/mL HepyC.00923.a.B1.PW38239 in 6 mM AMPPNP + magnesium chloride against Morpheus screen condition D12 with 12.5% PEG1000, 12.5% PEG 3350, 12.5% MPD, 20 mM alcohols (1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol), 0.1 M bicine/Trizma base, pH 8.5, crystal tracking ID 291403d12, unique puck ID rmz3-8