3J1T | pdb_00003j1t

High affinity dynein microtubule binding domain - tubulin complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ERR
experimental model	PDB	1JFF

Sample
High affinity construct of dynein microtubule binding domain bound to microtubules
Sample Components
dynein microtubule binding domain
alpha-tubulin
beta-tubulin

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	The solution was blotted manually, and the process of addition and blotting of SRS-MTBD was repeated a total of three times. The final blotting was do ...	The solution was blotted manually, and the process of addition and blotting of SRS-MTBD was repeated a total of three times. The final blotting was done inside the humidity chamber of a Vitrobot Mark IV (FEI) at 22 Celsius.

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	10419
Reported Resolution (Å)	9.7
Resolution Method
Other Details	Projection matching and Helical symmetry operator during reconstruction
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	9.26
Angular Rotation	-25.76

Map-Model Fitting and Refinement
Id	1 (3ERR)	2 (1JFF)	3 (1JFF)
Refinement Space	REAL	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--Molecular dynamics flexible fitting REFINEMENT PROTOCOL--Rigid body DETAILS--Explicit solvent molecular dynamics, molecular dynamics flexible ...	METHOD--Molecular dynamics flexible fitting REFINEMENT PROTOCOL--Rigid body DETAILS--Explicit solvent molecular dynamics, molecular dynamics flexible fitting, target molecular dynamics	METHOD--Molecular dynamics flexible fitting REFINEMENT PROTOCOL--Rigid body DETAILS--Explicit solvent molecular dynamics, molecular dynamics flexible ...	METHOD--Molecular dynamics flexible fitting REFINEMENT PROTOCOL--Rigid body DETAILS--Explicit solvent molecular dynamics, molecular dynamics flexible fitting	METHOD--Molecular dynamics flexible fitting REFINEMENT PROTOCOL--Rigid body DETAILS--Explicit solvent molecular dynamics, molecular dynamics flexible ...	METHOD--Molecular dynamics flexible fitting REFINEMENT PROTOCOL--Rigid body DETAILS--Explicit solvent molecular dynamics, molecular dynamics flexible fitting

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2011-04-10
Temperature (Kelvin)	100
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	62000
Calibrated Magnification	63377
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	NAMD
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	phase and amplitude correction using Frealign

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.