7BV8
Mature 50S ribosomal subunit from RrmJ knock out E.coli strain
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.875 |
| f_angle_d | 0.718 |
| f_chiral_restr | 0.043 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.005 |
| Sample |
|---|
| Mature 50S ribosomal subunit from RrmJ knock out E.coli strain |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 2 seconds before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 98194 |
| Reported Resolution (Å) | 3.14 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | A soft mask was added to improve resolution at the final refinement. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4YBB, 5H5U) | 2 (4YBB, 5H5U) | |||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 45 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | -1000 |
| Maximum Defocus (nm) | -2000 |
| 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 | 75000 |
| Calibrated Magnification | 75000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminary grid screening was performed manually. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 1.4 |
| CTF CORRECTION | CTFFIND | 3.0 |
| MODEL FITTING | UCSF Chimera | 1.13 |
| INITIAL EULER ASSIGNMENT | RELION | 1.4 |
| FINAL EULER ASSIGNMENT | RELION | 1.4 |
| CLASSIFICATION | RELION | 1.4 |
| RECONSTRUCTION | RELION | 1.4 |
| MODEL REFINEMENT | PHENIX | 1.16 |
| MODEL REFINEMENT | REFMAC | 5 |
| MODEL FITTING | UCSF Chimera | 1.13 |
| MODEL REFINEMENT | PHENIX | 1.16 |
| MODEL REFINEMENT | REFMAC | 5 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF amplitude correction was performed following 3D reconstruction. | 233762 | Images were binned and lowpass filtered for autopicking. | |
