ELECTRON MICROSCOPY Experimental Data



EM Sample
Sample Concentration (mg/ml) 0.2
Sample pH 7.4
Sample Support Details HOLEY CARBON
Sample Vitrification Details PLUNGED INTO ETHANE
Sample Buffer buf1
Sample Aggregation State FILAMENT
Name of Sample KIF1A HEAD DECORATED MICROTUBULE
Sample Details TUBULIN WAS POLYMERIZED IN PEM BUFFER (PIPES 100 MM, PH 6.8, EGTA 1 MM, MGCL2, GTP 1MM, PACLITAXEL 10 MICRO M, 5% DMSO ) FOR 2 HRS AT 37C. A DROP OF THE POLYMERIZED MICROTUBULE WAS PLACED ON THE HOLEY CARBON FILM ON THE EM-GRID AND LEFT FOR 10 S IN THE HUMID CHAMBER. THE MICROTUBULE SOLUTION WAS THEN ABSORBED BY FILTER PAPER, AND A DROP OF THE C351 SOLUTION (0.2 MG/ML) IN THE ASSAY BUFFER (IMIDAZOLE 50 MM, MG-ACETATE 5 MM, EGTA 1 MM, K-ACETATE 50 MM, DTT 10 MM, PACLITAXEL 10 MICRO M) WAS PUT ON THE GRID. IMMEDIATELY AFTER THE ABSORPTION OF THE DROP, THE GRID WAS PLUNGED INTO LIQUID ETHANE (-185C). THE SAMPLE CONSISTS OF A KIF1A-DECORATED MICROTUBULE. THE EXPERIMENT DESCRIBES A MICROTUBULE-RELATED PROCESS.
EM Data Acquisition
Date of Experiment 1998-07-01
Num of Micrographs-Images Used 130
Temperature (Kelvin) 110.0
Microscope Model JEOL JEM-2010F
Detector Type KODAK SO163 FILM
Minimum Defocus (nm) 1700.0
Maximum Defocus (nm) 3000.0
Minimum Tilt Angle (degrees) 0.0
Maximum Tilt Angle (degrees) 2.0
Nominal CS 3.3
Imaging Mode BRIGHT FIELD
Electron Dose (electrons nm**-2) 1000.0
Illumination Mode FLOOD BEAM LOW DOSE
Nominal Magnification 40000
Calibrated Magnification --
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details --
3D Reconstruction
Software Package(s)
Reconstruction Method
EM Image Reconstruction Statistics
Number of Particles 37000
Nominal Pixel Size 2.5
Effective Resolution 15.0
Other Details THREE-DIMENSIONAL RECONSTRUCTION METHOD: FOURIER-BESSEL-TRANSFORM (DEROSIER AND MOORE, 1970 J.MOL.BIOL. 52, 355-369; BEROUKHIM AND UNWIN, 1997 ULTRAMICROSCOPY 70, 57-81). Software used: MRC PROGRAMS. EFFECTIVE RESOLUTION OF THE RECONSTRUCTION: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 15 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND CALCULATING THE FOURIER SHELL CORRELATIONS BETWEEN THE TWO INDEPENDENT SET. (HEEL, 1987, ULTRAMICROSCOPY 21, 95-100). 1IA0 is an atomic model of KIF1A head-microtubule complex, which contains KIF1A, alpha-tubulin, and beta-tubulin. Since alpha- and beta-tubulin were indistinguishable at 15A resolution, the assignment of alpha- and beta-tubulin was arbitrary when 1IA0 was deposited. Authors state that they were aware of the limitation and didn't mention about the assignment of alpha- and beta-tubulin in the relevant 2001 Nature paper. Therefore, the main conclusions in the paper are still hold true. However, subsequently the assignment of alpha- and beta-tubulin turned out to be wrong and should be swapped. For the correct assignment and better structures, please use 2HXF. This is based on higher resolution (10 ) structure, which was published in EMBO J. 2006. 25:4187-4194.
EM Map-Model Fitting and Refinement
Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Fitting Software
REAL RIGID BODY REFINEMENT MAXIMUM CORRELATION -- -- --