6ZI0

Crystal structure of the isolated H. influenzae VapD toxin (wildtype)

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-03-22
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.98021
Spacegroup name	P 63 2 2
Unit cell lengths	99.100, 99.100, 44.470
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	85.882 - 2.500
Rwork	0.220
R-free	0.26360
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6HKD
RMSD bond length	0.008
RMSD bond angle	1.741
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	REFMAC (5.8.0253)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	85.882	85.882	2.560
High resolution limit [Å]	2.500	11.180	2.500
Rmerge	0.212	0.036	1.581
Rmeas	0.223	0.038	1.659
Number of reflections	4800	74	344
<I/σ(I)>	9.49	29.4	1.33
Completeness [%]	99.9	98.7	100
Redundancy	10.357	7.189	10.677
CC(1/2)	0.996	1.000	0.546

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	4	292	1 M LiCl, 0.1 M citrate, 20% PEG 6000