7NT6
CryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7NT5 |
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 |
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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 |
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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 |