7NT6
CryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 35.24 |
| r_mcangle_it | 28.663 |
| r_mcbond_it | 19.206 |
| r_scbond_it | 14.11 |
| r_dihedral_angle_1_deg | 8.138 |
| r_angle_refined_deg | 1.96 |
| r_chiral_restr | 0.123 |
| r_bond_refined_d | 0.011 |
| r_gen_planes_refined | 0.01 |
| r_bond_other_d | |
| Sample |
|---|
| Nipah virus nucleocapsid Protein-RNA complex |
| Sample Components |
| Nucleoprotein |
| RNA (48-MER) |
| RNA (42-MER) |
| 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 | 23029 |
| Reported Resolution (Å) | 4.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7NT5) | ||||
| Refinement Space | |||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 41 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 2100 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.0 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | UCSF Chimera | 1.13 |
| CLASSIFICATION | RELION | 3.1beta |
| RECONSTRUCTION | RELION | 3.1beta |
| MODEL REFINEMENT | REFMAC | 5.8.0267 |
| MODEL REFINEMENT | PHENIX | 1.17 |
| MODEL REFINEMENT | ERRASER | 2 |
| MODEL REFINEMENT | ISOLDE | 0.9 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 217522 | |||
