6ZI1

Crystal structure of the isolated H. influenzae VapD toxin (D7N mutant)

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	2019-11-26
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.98021
Spacegroup name	P 3 2 1
Unit cell lengths	84.380, 84.380, 49.480
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	42.226 - 2.200
Rwork	0.214
R-free	0.26660
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	D_1292109585
RMSD bond length	0.007
RMSD bond angle	1.484
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER (2.8.3)
Refinement software	REFMAC (5.8.0253)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	42.226	42.226	2.260
High resolution limit [Å]	2.200	9.840	2.200
Rmerge	0.060	0.021	0.928
Rmeas	0.071	0.024	1.122
Number of reflections	10306	120	736
<I/σ(I)>	12.11	49.94	1.31
Completeness [%]	97.2	85.1	97.9
Redundancy	3.334	3.067	3.096
CC(1/2)	0.999	0.999	0.612

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6	292	50 mM Na cacodylate, 1.8 M ammonium sulphate