6ZI0

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	292	1 M LiCl, 0.1 M citrate, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.1	α = 90
b = 99.1	β = 90
c = 44.47	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2019-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.98021	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	85.882	99.9	0.212	0.223	0.996	9.49	10.357		4800			44.739

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56	100		1.581	1.659	0.546	1.33	10.677

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6HKD	2.5	85.882	4800	241	99.917	0.222	0.2202	0.2636	76.248

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.869	0.435		0.869		-2.821

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.995
r_dihedral_angle_4_deg	25.709
r_dihedral_angle_3_deg	18.109
r_lrange_it	16.647
r_lrange_other	16.564
r_scangle_it	11.133
r_scangle_other	11.13
r_mcangle_other	9.815
r_mcangle_it	9.803
r_dihedral_angle_1_deg	8.513
r_scbond_it	7.744
r_scbond_other	7.435
r_mcbond_it	6.859
r_mcbond_other	6.646
r_angle_refined_deg	1.741
r_angle_other_deg	1.24
r_symmetry_xyhbond_nbd_refined	0.256
r_symmetry_nbd_refined	0.255
r_nbd_other	0.238
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.167
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	722
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
PHASER	phasing
XSCALE	data scaling