7PTL
Mature conformer of a 6-helix bundle of RNA with clasp
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 16.002 |
| f_angle_d | 1.003 |
| f_chiral_restr | 0.06 |
| f_plane_restr | 0.007 |
| f_bond_d | 0.005 |
| Sample |
|---|
| Mature conformer of a 6-helix bundle of RNA with clasp |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 microlitre droplet, 4 second delay before blotting, 6 second blot, 0 second delay before plunging. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 337099 |
| Reported Resolution (Å) | 4.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2D1B) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Correlation Coefficient | ||||
| Overall B Value | 303 | ||||
| Fitting Procedure | |||||
| Details | Helical templates and tetraloops were generated in RNAbuild. Kissing loops were modelling based on the PDB:2D1B structure. A combination of PHENIX RSR ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 750 |
| Maximum Defocus (nm) | 2500 |
| 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 | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.2.0 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 3.2.0 |
| MODEL FITTING | UCSF ChimeraX | 1.2 |
| MODEL FITTING | ISOLDE | 1.2 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158-000 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
| CLASSIFICATION | cryoSPARC | 3.2.0 |
| RECONSTRUCTION | cryoSPARC | 3.2.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF estimation (multi) from cryoSPARC. | 1476537 | Particle picking was performed using the template picker from cryoSPARC with templates generated from an ab initio model from the same dataset. | |
