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 3J1U | pdb_00003j1u

Low affinity dynein microtubule binding domain - tubulin complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ERR 
experimental modelPDB 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 StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsThe 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 MethodHELICAL
Number of Particles10419
Reported Resolution (Å)9.7
Resolution Method
Other DetailsProjection matching and Helical symmetry operator during reconstruction
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise9.26
Angular Rotation-25.76
Map-Model Fitting and Refinement
Id1 (3ERR)2 (1JFF)3 (1JFF)
Refinement SpaceREALREALREAL
Refinement ProtocolRIGID BODY FITFLEXIBLE FITFLEXIBLE FIT
Refinement TargetMolecular dynamics force field
Overall B Value
Fitting Procedure
DetailsMETHOD--Molecular dynamics equilibration REFINEMENT PROTOCOL--Rigid body DETAILS--explicit solvent molecular dynamicsMETHOD--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 TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)15
Imaging Experiment1
Date of Experiment2011-04-10
Temperature (Kelvin)100
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)500
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification62000
Calibrated Magnification63377
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)120
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGNAMD
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
phase and amplitude correction using Frealign