9GCL
Structure of the U11 snRNP C-lobe
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| in silico model | AlphaFold | AF-Q9UDW3-F1 | |
| in silico model | AlphaFold | AF-Q6IEG0-F1 | |
| experimental model | PDB | 4PJO | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 14.3666 |
| f_angle_d | 0.659 |
| f_chiral_restr | 0.0415 |
| f_plane_restr | 0.0051 |
| f_bond_d | 0.003 |
| Sample |
|---|
| Structure of the apo-U11 snRNP 3-lobe |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 222666 |
| Reported Resolution (?) | 3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4PJO, 4PJO, 4PJO, 4PJO, 4PJO, 4PJO, 4PJO) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correction coefficient | ||||
| Overall B Value | 71.2 | ||||
| Fitting Procedure | |||||
| Details | refinement is done in Phenix | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/?**2) | 41.73 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 1700 |
| 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 | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminary grid screening was performed on Glacios. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v4.3.1 |
| IMAGE ACQUISITION | SerialEM | |
| MODEL FITTING | UCSF ChimeraX | 1.6.1 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v4.3.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v4.3.1 |
| CLASSIFICATION | cryoSPARC | v4.3.1 |
| RECONSTRUCTION | cryoSPARC | v4.3.1 |
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 7144222 | Topaz picking is performed with user-trained model | ||
