4PU8

Shewanella oneidensis Toxin Antitoxin System Antitoxin Protein HipB Resolution 2.35


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DNVpdb entry 3DNV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1M Na HEPES pH7.5, 10% v/v 2-propanol, 20% PEG 4000, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.5922.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.57α = 90
b = 71.57β = 90
c = 85.81γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3538.3699.7145147126742.15

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 3DNV2.3538.361.34712533599.710.20490.2040.2238
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.042
f_angle_d0.878
f_chiral_restr0.046
f_bond_d0.004
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1070
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement