6ZI1 | pdb_00006zi1

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZI0	D_1292109585

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	292	50 mM Na cacodylate, 1.8 M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.38	α = 90
b = 84.38	β = 90
c = 49.48	γ = 120

Symmetry
Space Group	P 3 2 1

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		2019-11-26	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	2.2	42.226	97.2	0.06	0.071	0.999	12.11	3.334		10306			53.573

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	2.2	2.26	97.9		0.928	1.122	0.612	1.31	3.096

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	D_1292109585	2.2	42.226	10306	1028	97.227	0.22	0.2145	0.22	0.2666	0.27	58.862

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]
0.876	0.438		0.876		-2.842

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.923
r_dihedral_angle_4_deg	23.103
r_dihedral_angle_3_deg	20.082
r_lrange_it	17.508
r_lrange_other	17.478
r_scangle_it	9.149
r_scangle_other	9.134
r_mcangle_it	7.78
r_mcangle_other	7.778
r_dihedral_angle_1_deg	7.316
r_scbond_it	5.796
r_scbond_other	5.773
r_mcbond_it	4.931
r_mcbond_other	4.931
r_angle_refined_deg	1.484
r_angle_other_deg	1.285
r_symmetry_nbd_refined	0.348
r_nbd_other	0.296
r_nbd_refined	0.257
r_xyhbond_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.214
r_nbtor_refined	0.175
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1333
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction