3ZBJ
Fitting results in the I-layer of the subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase
ELECTRON MICROSCOPY
Sample |
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TRAN, TRAO AND TRAF COMPLEX ENCODED BY PKM101 DIGESTED WITH 0.02 MG ML- 1 OF ELASTASE FOR 40 MIN AT ROOM TEMPERATURE |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK III |
Cryogen Name | ETHANE |
Sample Vitrification Details | VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 92, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT 4 SECONDS BEFORE PLUNGING, |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 5430 |
Reported Resolution (Å) | 8.5 |
Resolution Method | |
Other Details | SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2233. (DEPOSITION ID: 11228). |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C14 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | METHOD--RIGID BODY FOLLOWED BY FLEXIBLE FITTING REFINEMENT PROTOCOL--MODELLED |
Data Acquisition | |||||||||
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Detector Type | GENERIC GATAN | ||||||||
Electron Dose (electrons/Å**2) | 20 |
Imaging Experiment | 1 |
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Date of Experiment | 2012-01-11 |
Temperature (Kelvin) | 95 |
Microscope Model | FEI TECNAI 12 |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 3500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.1 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | 66000 |
Calibrated Magnification | 68100 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details | 4000X4000 CCD |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | Flex-EM | |
MODEL FITTING | Sculptor | |
MODEL FITTING | Situs | |
MODEL FITTING | UCSF Chimera | |
RECONSTRUCTION | IMAGIC |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING, EACH CCD IMAGE |