7KTX
Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to a Fab in DDM detergent
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 18.0758 |
| f_angle_d | 0.9884 |
| f_chiral_restr | 0.0552 |
| f_plane_restr | 0.0069 |
| f_bond_d | 0.0057 |
| Sample |
|---|
| S. cerevisiae endoplasmic reticulum membrane protein complex (EMC) bound to Fab in DDM detergent |
| Sample Components |
| endoplasmic reticulum membrane protein complex |
| Fab DH4 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 83599 |
| Reported Resolution (Å) | 4.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | These two datasets were processed independently initially. Upon selecting the best subset of data and then re-extracted and scaled to the same pixel ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Number of Particles | 170186 |
| Reported Resolution (Å) | 4.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | GATAN K2 SUMMIT (4k x 4k) | |||||||
| Electron Dose (electrons/Å**2) | 56.8 | 58.3 | |||||||
| Imaging Experiment | 1 | 2 |
|---|---|---|
| Date of Experiment | ||
| Temperature (Kelvin) | ||
| Microscope Model | FEI POLARA 300 | FEI TITAN KRIOS |
| Minimum Defocus (nm) | ||
| Maximum Defocus (nm) | ||
| Minimum Tilt Angle (degrees) | ||
| Maximum Tilt Angle (degrees) | ||
| Nominal CS | ||
| Imaging Mode | BRIGHT FIELD | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER | |
| Nominal Magnification | ||
| Calibrated Magnification | ||
| Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 | 300 |
| Imaging Details | Dataset 1 collected on FEI Polara at UCSF on August 22nd, 2016. | Dataset 2 collected on FEI Titan Krios at Janelia Research Campus on October 20th, 2016. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Leginon | |
| IMAGE ACQUISITION | SerialEM | |
| INITIAL EULER ASSIGNMENT | RELION | |
| INITIAL EULER ASSIGNMENT | RELION | |
| MODEL REFINEMENT | PHENIX | 1.18 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
