7PTU
Structure of pentameric S-layer protein from Halofaerax volcanii
ELECTRON MICROSCOPY
Sample |
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Structure of pentameric S-layer protein csg |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Vitrobot options: Blot time 5 seconds, Blot force -10,1, Wait time 10 seconds, Drain time 0.5 seconds |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 382105 |
Reported Resolution (Å) | 3.87 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | The final map (RELION3.1) was obtained from 382,105 particles and post-processed using a soft mask focused on the entire pentameric map yielding a glo ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C5 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | Best Fit | ||||
Overall B Value | 179.68 | ||||
Fitting Procedure | |||||
Details | The initial manual build of D1-D2 was performed independently using the csg pentameric cryo-EM map, which served as an additional validation of the ma ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 53.9 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 4000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 81000 |
Calibrated Magnification | 81000 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | EPU software with faster acquisition mode AFIS (Aberration Free Image Shift). |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | RELION | 3.0 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.1.13 |
MODEL FITTING | Coot | 0.9.2-pre |
INITIAL EULER ASSIGNMENT | RELION | 3.0 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
MODEL REFINEMENT | PHENIX | 1.19-4092 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included. | 1773652 | Particles were initially picking using the Laplacian-of gaussian algorithm implemented in RELION3.0 (Zivanov et al., 2018). Particles were extracted in 8x down-sampled in 50x50 pixel boxes and classified using reference-free 2D classification inside RELION3.0. |