8QN6
Amyloid-beta 40 type 2 filament from the leptomeninges of individual with Alzheimer's disease and cerebral amyloid angiopathy
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7Q4B |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_other | 15.005 |
r_long_range_B_refined | 14.991 |
r_scangle_other | 10.483 |
r_dihedral_angle_3_deg | 8.991 |
r_mcangle_other | 7.071 |
r_mcangle_it | 7.054 |
r_scbond_it | 6.259 |
r_scbond_other | 6.249 |
r_dihedral_angle_1_deg | 5.263 |
r_mcbond_it | 4.574 |
Sample |
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Amyloid-beta 40 |
Specimen Preparation | |
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Sample Aggregation State | FILAMENT |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | HELICAL |
Number of Particles | 81140 |
Reported Resolution (Å) | 2.4 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C2 |
Axial Rise | 4.87 |
Angular Rotation | -0.78 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (7Q4B) | ||||
Refinement Space | |||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2400 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | 4.0 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | RELION | |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | RELION | |
FINAL EULER ASSIGNMENT | RELION | |
CLASSIFICATION | RELION | |
RECONSTRUCTION | RELION | |
MODEL REFINEMENT | REFMAC | |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |