1JFF | pdb_00001jff

Refined structure of alpha-beta tubulin from zinc-induced sheets stabilized with taxol

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	aberrant polymerization of tubulin	5.8	305	Zn++, pH 5.8, aberrant polymerization of tubulin, temperature 305K

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	93	FILM	KODAK		1994-01-01	M	SINGLE WAVELENGTH
2	1		CCD	GATAN

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	JEOL 4000 electron microscope	0.0194

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.5	20	73	0.25	5.4	6	12422	12422			40

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.5	3.7	73		2.3		1080

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	PDB entry 1TUB	3.5	20	12422	12422	623		0.2315	0.2966	random	41.4

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]
26.5			10.8		-37.4

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_d	1.561
c_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6578
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	124

Software

Software
Software Name	Purpose
CCP4	model building
CNS	refinement
CCP4	phasing

Sample
Alpha-Beta-tubulin sheets

Specimen Preparation
Sample Aggregation State	2D ARRAY
Vitrification Instrument
Cryogen Name	NITROGEN
Sample Vitrification Details
Embedding Material	tannin
Embedding Details

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY

Data Acquisition
Detector Type	GENERIC FILM
Electron Dose (electrons/Å**2)

Imaging Experiment	1	2
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL 4000	JEOL 4000
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD	DIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
Acceleration Voltage (kV)
Imaging Details

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.