3JBI
MDFF model of the vinculin tail domain bound to F-actin
ELECTRON MICROSCOPY
Sample |
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Vinculin tail domain bound to F-actin |
Sample Components |
skeletal muscle actin |
Vinculin tail domain, residues 879-1061 |
Specimen Preparation | |
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Sample Aggregation State | FILAMENT |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar Vt was then ... |
3D Reconstruction | |
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Reconstruction Method | HELICAL |
Number of Particles | |
Reported Resolution (Å) | 8.5 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | (Helical Details: Single model IHRSR was performed with EMAN2 / SPARX and final reconstruction with FREALIGN (fixed helical parameters).) |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 27.8 |
Angular Rotation | 166.82 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1QKR) | 2 (3J8A) | |||
Refinement Space | REAL | REAL | |||
Refinement Protocol | FLEXIBLE FIT | FLEXIBLE FIT | |||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | REFINEMENT PROTOCOL--flexible DETAILS--Components were initially rigid body fit using Chimera, followed by flexible fitting with MDFF. | REFINEMENT PROTOCOL--flexible DETAILS--Components were initially rigid body fit using Chimera, followed by flexible fitting with MDFF. |
Data Acquisition | |||||||||
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Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 25 |
Imaging Experiment | 1 |
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Date of Experiment | 2014-05-22 |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI F20 |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 3000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN LIQUID NITROGEN |
Nominal Magnification | 100000 |
Calibrated Magnification | 137615 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 120 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
CTF CORRECTION | CTFFIND | 3 |
MODEL FITTING | MDFF | |
MODEL FITTING | UCSF Chimera | |
RECONSTRUCTION | EMAN | 2 |
RECONSTRUCTION | FREALIGN | |
RECONSTRUCTION | SPARX |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
FREALIGN (per segment) |