3TND | pdb_00003tnd

Crystal structure of Shigella flexneri VapBC toxin-antitoxin complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	0.1M Bis-tris, 1M ammonium sulphate, 0.5% (v/v) PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.403	α = 90
b = 91.403	β = 90
c = 549.09	γ = 120

Symmetry
Space Group	P 61 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	CCD	ADSC QUANTUM 315r		2011-04-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm		2011-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.94645	ESRF	ID23-1
2	SYNCHROTRON	MAX II BEAMLINE I911-2	1.04002	MAX II	I911-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.6	40	99.7			43852	43720		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.6	2.66	97.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	2.7	39.615	43720	38932	1783	99.93	0.1849	0.1824	0.1769	0.2375	0.2306

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]
5.7565			5.7565		-11.5131

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.439
f_angle_d	0.838
f_chiral_restr	0.056
f_bond_d	0.005
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6280
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	57

Software

Software
Software Name	Purpose
DNA	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling