4U6F

Crystal structure of T-2 toxin bound to the yeast 80S ribosome


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U5B3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental modelPDB 3U5C3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental modelPDB 3U5D3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental modelPDB 3U5E3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental modelPDB 3U5F3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental modelPDB 3U5G3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental modelPDB 3U5H3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I
experimental modelPDB 3U5I3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Crystal Properties
Matthews coefficientSolvent content
3.0759.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 436.64α = 90
b = 287.69β = 98.98
c = 304.39γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 11.0SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.9300.6698.80.4010.4364.195.691614049-371.82
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.9398.53.8394.2590.49

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3U5B, 3U5C, 3U5D, 3U5E, 3U5F, 3U5G, 3U5H, 3U5I3.1300.6613208862641798.70.19880.19780.246768.1262
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_d18.959
f_angle_d1.513
f_chiral_restr0.06
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms179692
Nucleic Acid Atoms222781
Solvent Atoms
Heterogen Atoms10988

Software

Software
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XSCALEdata reduction