7AE2

Crystal structure of HEPN(H107A-Y109F) toxin in complex with MNT antitoxin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291Crystallization buffer was 0,1 M MES-imidazole pH 6.5, 10% PEG 20K, 20% PEG550MME, 30 mM NaNO3, 30 mM Na2HPO4, 30 mM(NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.709α = 90
b = 85.989β = 90
c = 100.105γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2018-05-17MSINGLE WAVELENGTH
21x-ray100PIXELPSI PILATUS 6M2018-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.3862PETRA III, EMBL c/o DESYP13 (MX1)
2SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.979600PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
1255.52199.90.0410.0490.01922.36.4215392153941.17
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1199.90.4580.4580.5290.2061.56.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT250.0530.2621501409899.560.20190.19920.226658.0177
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_d11.94
f_angle_d0.437
f_chiral_restr0.038
f_plane_restr0.003
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2184
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
PDB_EXTRACTdata extraction