5LZS
Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.376 |
| r_dihedral_angle_1_deg | 27.114 |
| r_long_range_B_refined | 23.079 |
| r_long_range_B_other | 23.079 |
| r_dihedral_angle_3_deg | 16.286 |
| r_dihedral_angle_4_deg | 13.339 |
| r_mcangle_it | 7.147 |
| r_mcangle_other | 7.147 |
| r_scangle_other | 6.08 |
| r_mcbond_it | 3.999 |
| Sample |
|---|
| Affinity-purified 80S ribosome-nascent chain complex stalled with didemnin B and containing aminoacyl-tRNA and eEF1A. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 40347 |
| Reported Resolution (Å) | 3.31 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | FSCaverage | ||||
| Overall B Value | 64.8 | ||||
| Fitting Procedure | |||||
| Details | Restraints for didemnin B were derived from Phenix.elbow and Mogul. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| 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 | 69000 |
| Calibrated Magnification | 134615 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | EMAN | 2 |
| PARTICLE SELECTION | RELION | 1.4 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | 0.5 |
| MODEL FITTING | UCSF Chimera | 1.10 |
| MODEL FITTING | Coot | 5.8 |
| INITIAL EULER ASSIGNMENT | RELION | 1.4 |
| FINAL EULER ASSIGNMENT | RELION | 1.4 |
| CLASSIFICATION | RELION | 1.4 |
| RECONSTRUCTION | RELION | 1.4 |
| MODEL REFINEMENT | REFMAC | 5.8 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 139655 | |||
