5V6D

Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate

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	2016-10-26
Detector	MARMOSAIC 225 mm CCD
Wavelength(s)	0.97872
Spacegroup name	P 1
Unit cell lengths	57.240, 112.350, 112.870
Unit cell angles	104.31, 98.50, 105.39

Refinement procedure

Resolution	44.089 - 1.850
R-factor	0.1504
Rwork	0.150
R-free	0.18840
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3vgs
RMSD bond length	0.006
RMSD bond angle	0.755
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	50.000	1.900
High resolution limit [Å]	1.850	8.270	1.850
Rmerge	0.060	0.034	0.517
Rmeas	0.074	0.043	0.630
Number of reflections	212120	2296	15507
<I/σ(I)>	11.92	28.28	2.6
Completeness [%]	97.1	94.2	96.2
Redundancy	2.972	2.832	2.985
CC(1/2)	0.997	0.996	0.891

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5	290	17.1 mg/mL NegoA.00438.a.B1.PW37901 + JCSG+ screen B9: 20% PEG6000, 100 mM sodium citrate tribasic, pH 5.0, cryoprotectant: 20% ethylene glycol in two steps, tray 2273617b9, puck mrl5-6