1TVK

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

ELECTRON CRYSTALLOGRAPHY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JFF

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
	66.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.2	α = 90
b = 93.5	β = 90
c = 90	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron						M	SINGLE WAVELENGTH

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		THROUGHOUT	PDB ID 1JFF	2.89	91.29	18321	18321	967	67.03	0.33214	0.33214	0.33275	0.32096	RANDOM	79.8

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]
-5.48		0.41	-3.03		8.5

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6578
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	94

Sample
tubulin 2D crystal

Specimen Preparation
Sample Aggregation State	2D ARRAY

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	2.89
Resolution Method
Other Details
Refinement Type
Symmetry Type	2D CRYSTAL

Map-Model Fitting and Refinement
Id	1 (1JFF)
Refinement Space	RECIPROCAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Analysis of comparitive difference densities
Overall B Value
Fitting Procedure
Details	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 Type	GENERIC GATAN
Electron Dose (electrons/Å**2)	100

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	100
Microscope Model	JEOL 4000EX
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)	15
Maximum Tilt Angle (degrees)	55
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
Acceleration Voltage (kV)	400
Imaging Details	A 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
Task	Software Package	Version
MODEL FITTING	CNS	1.1
MODEL FITTING	QUANTA
MODEL FITTING	REFMAC	5
RECONSTRUCTION	MRC