3JC1
Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FRR |
Sample |
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IST1-NTD and CHMP1B double-stranded helical filament |
Sample Components |
IST1 |
CHMP1B |
Specimen Preparation | |
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Sample Aggregation State | FILAMENT |
Vitrification Instrument | FEI VITROBOT MARK III |
Cryogen Name | ETHANE |
Sample Vitrification Details | Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset), and plunged into liquid ethane (VITROBOT MARK III). |
3D Reconstruction | |
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Reconstruction Method | HELICAL |
Number of Particles | 188713 |
Reported Resolution (Å) | 4 |
Resolution Method | |
Other Details | Modified version of IHRSR algorithms as implemented in SPIDER was used to determine the helical symmetry. 3D reconstructions were performed using RELI ... |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 2.96 |
Angular Rotation | 21.06 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (3FRR) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | |||||
Refinement Target | Molprobity validation, cross-correlation | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | DETAILS--IST1 starting model (3FRR) was idealized in Rosetta, then relaxed while the structure was constrained. Iterative loop building was used. |
Data Acquisition | |||||||||
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Detector Type | KODAK SO-163 FILM | ||||||||
Electron Dose (electrons/Å**2) | 20 |
Imaging Experiment | 1 | 2 | 3 |
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Date of Experiment | 2013-06-01 | 2013-06-01 | 2013-06-01 |
Temperature (Kelvin) | |||
Microscope Model | FEI TITAN KRIOS | FEI TECNAI F20 | JEOL 3200FSC |
Minimum Defocus (nm) | 600 | 600 | 600 |
Maximum Defocus (nm) | 3000 | 3000 | 3000 |
Minimum Tilt Angle (degrees) | |||
Maximum Tilt Angle (degrees) | |||
Nominal CS | 2 | 2 | 3.4 |
Imaging Mode | BRIGHT FIELD | BRIGHT FIELD | BRIGHT FIELD |
Specimen Holder Model | |||
Nominal Magnification | 59000 | 50000 | 59000 |
Calibrated Magnification | |||
Source | FIELD EMISSION GUN | FIELD EMISSION GUN | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 | 200 | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
CTF CORRECTION | CTFFIND | 3 |
MODEL FITTING | Coot | |
MODEL FITTING | MDFF | |
MODEL FITTING | NAMD | |
MODEL FITTING | Rosetta | |
MODEL FITTING | UCSF Chimera | |
RECONSTRUCTION | EMAN | 2 |
RECONSTRUCTION | IHRSR | |
RECONSTRUCTION | RELION | |
RECONSTRUCTION | SPIDER |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
CTFFIND3 |