ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7JPT | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.5873 |
| f_angle_d | 0.628 |
| f_chiral_restr | 0.0428 |
| f_plane_restr | 0.0045 |
| f_bond_d | 0.0031 |
| Sample |
|---|
| Human PLA2R Ectodomain |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 2D ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 221000 |
| Reported Resolution (Å) | 3.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7JPT) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation Coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | GATAN K3 (6k x 4k) | |||||||
| Electron Dose (electrons/Å**2) | 14.8 | 14.2 | |||||||
| Imaging Experiment | 1 | 2 |
|---|---|---|
| Date of Experiment | ||
| Temperature (Kelvin) | ||
| Microscope Model | FEI TITAN KRIOS | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 | 800 |
| Maximum Defocus (nm) | 2000 | 2000 |
| Minimum Tilt Angle (degrees) | ||
| Maximum Tilt Angle (degrees) | ||
| Nominal CS | ||
| Imaging Mode | BRIGHT FIELD | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | ||
| Calibrated Magnification | ||
| Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 | 300 |
| Imaging Details | 30 degree Tilt dataset |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | PHENIX | 1.19.2 |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1700000 | Particles were picked using a Gaussian blob (80-130 ang) from 100 images of the 0 deg data set were extracted in a 256 pixel box, binned 4x4 (64 pixel box), and subjected to 2D classification. The best templates were used to template pick all images from both data sets. | ||
