3JD5
Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 9.401 |
| f_angle_d | 0.304 |
| f_chiral_restr | 0.028 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.001 |
| Sample |
|---|
| small subunit of mitochondrial ribosome |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Plunged into liquid ethane (FEI VITROBOT MARK I). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 307556 |
| Reported Resolution (Å) | 7 |
| Resolution Method | |
| Other Details | A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classi ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5AJ3, 3J9M) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--Flexible fitting REFINEMENT PROTOCOL--rigid body | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN ULTRASCAN 1000 (2k x 2k) | ||||||||
| Electron Dose (electrons/Å**2) | 9 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2009-10-10 |
| Temperature (Kelvin) | 100 |
| Microscope Model | JEOL 3200FS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 4500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN LIQUID NITROGEN |
| Nominal Magnification | 60000 |
| Calibrated Magnification | 59717 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | MDFF | |
| RECONSTRUCTION | RELION | 1.2 |
| RECONSTRUCTION | SPIDER | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| CTFFIND3 | ||||
