6Z61

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE MASSIF-1
Synchrotron site	ESRF
Beamline	MASSIF-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-07-16
Detector	DECTRIS PILATUS3 2M
Wavelength(s)	0.966
Spacegroup name	I 2 2 2
Unit cell lengths	62.585, 75.423, 118.131
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	59.070 - 2.470
R-factor	0.2222
Rwork	0.220
R-free	0.27930
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6rg9
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHENIX
Refinement software	PHENIX (1.17.1_3660)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	59.070	59.065	2.372
High resolution limit [Å]	2.241	6.794	2.241
Rmerge	0.060	0.035	0.694
Rmeas	0.063	0.037	0.821
Rpim	0.019	0.012	0.423
Total number of observations		6046	1959
Number of reflections	11262	561	563
<I/σ(I)>	22.1	62.8	1.5
Completeness [%]	89.0	100	43.2
Redundancy	9.9	10.8	3.5
CC(1/2)	0.999	0.999	0.700

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		291.15	30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400