1TVK

The binding mode of epothilone A on a,b-tubulin by electron crystallography


ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JFF 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
66.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.2α = 90
b = 93.5β = 90
c = 90γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11electron MSINGLE WAVELENGTH

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
ELECTRON CRYSTALLOGRAPHYTHROUGHOUTPDB ID 1JFF2.8991.29183211832196767.030.332140.332140.332750.32096RANDOM79.8
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]
-5.480.41-3.038.5
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6578
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms94
Sample
tubulin 2D crystal
Specimen Preparation
Sample Aggregation State2D ARRAY
3D Reconstruction
Reconstruction MethodCRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)2.89
Resolution Method
Other Details
Refinement Type
Symmetry Type2D CRYSTAL
Map-Model Fitting and Refinement
Id1 (1JFF)
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetAnalysis of comparitive difference densities
Overall B Value
Fitting Procedure
DetailsMETHOD--annealing, rigid refining REFINEMENT PROTOCOL--rigid body DETAILS--THE MODEL WAS DERIVED USING HIGH RESOLUTION ELECTRON DIFFRACTIONS FROM TWO ...METHOD--annealing, rigid refining REFINEMENT PROTOCOL--rigid body DETAILS--THE MODEL WAS DERIVED USING HIGH RESOLUTION ELECTRON DIFFRACTIONS FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR EPOLTHILONE-A BOUND TO AB-TUBULIN DIMER IN THE ZINC-INDUCED SHEETS. THE LIGAND MODEL WAS FIT INTO A DENSITY MAP FOR WHICH THE RESOLUTION IN THE PLANE OF THE SHEET WAS 2.89 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET WAS ABOUT 4.2 ANGSTROMS AS DESCRIBED IN THE SUPPLEMENTARY MATERIAL. PHASES WERE DERIVED FROM A PREVIOUS MODEL OF ALPHA/BETA TUBULIN COMPLEXED WITH TAXOL (1JFF). SHAKING, HIGH TEMPERATURE ANANEALING, AND MODEL WERE COMBINED TO PRODUCE AN OMIT MAP OF THE BOUND EPOTHILONE THAT SYSTEMATIC BIAS.A NUMBER OF CONFORMATIONAL MODELS WERE FLEXIBLY FITTED INITIAL MAP AND TESTED AGAINST THE DIFFRACTIONS BY DIFFERENCE MAP AS DESCRIBED IN THE PRIMARY REFERENCE. REFINEMENT TO THE FINAL STAGE WAS LIMITED WITHIN AN 8A RADIUS OF THE LIGAND. ALTHOUGH THE REMAINING PART OF THE PROTEIN SHOWS LITTLE DEVIATION FROM THAT SEEN IN 1JFF, CER NOT FULLY CONFORM WITH RAMACHANDRAN CHARACTERISTICS. AND SHOULD B THE FINAL MAPS ASSOCIATED WITH THE PRESENT MODEL WERE DERIVED BY COMPLEX. AS SUCH, FREE R REPORTED BY THE SOFTWARE BELOW IS NOT RE
Data Acquisition
Detector TypeGENERIC GATAN
Electron Dose (electrons/Å**2)100
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)100
Microscope ModelJEOL 4000EX
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)15
Maximum Tilt Angle (degrees)55
Nominal CS
Imaging ModeDIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
Acceleration Voltage (kV)400
Imaging DetailsA weak electron beam and long exposure time (40-60s) were used to minimize the vertical blooming streak in the diffraction pattern recorded with the CCD camera.
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCNS1.1
MODEL FITTINGQUANTA
MODEL FITTINGREFMAC5
RECONSTRUCTIONMRC