3J2B
Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3OFA |
Sample |
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immature ribosomal small subunit from rimm gene deleted E.coli strain |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 30892 |
Reported Resolution (Å) | 13.6 |
Resolution Method | FSC 0.5 CUT-OFF |
Other Details | This is a classification volume (No. 4) using ML3D methods. ) |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (3OFA) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | REFINEMENT PROTOCOL--Initial local fitting was done using Chimera and then MDFF was used for flexible fitting DETAILS--ref- Trabuco, L.G., Villa, E., ... |
Data Acquisition | |||||||||
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Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 20 |
Imaging Experiment | 1 |
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Date of Experiment | 2012-01-01 |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI F20 |
Minimum Defocus (nm) | 1300 |
Maximum Defocus (nm) | 4000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN LIQUID NITROGEN |
Nominal Magnification | 80000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | MDFF | |
RECONSTRUCTION | SPIDER |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
Weiner filter |