9CVE
Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein VP1 5-12-18
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8VG6 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.664 |
f_angle_d | 0.58 |
f_chiral_restr | 0.056 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Sample |
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Tulane virus |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 10827 |
Reported Resolution (Å) | 3.18 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (8VG6) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 23 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2200 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | OTHER |
Specimen Holder Model | |
Nominal Magnification | 81000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
CTF CORRECTION | cryoSPARC | |
MODEL FITTING | Coot | 0.9 |
MODEL FITTING | UCSF ChimeraX | |
INITIAL EULER ASSIGNMENT | cryoSPARC | 4.0.0 |
FINAL EULER ASSIGNMENT | cryoSPARC | 4.0.0 |
CLASSIFICATION | cryoSPARC | 4.0.0 |
RECONSTRUCTION | cryoSPARC | 4.0.0 |
MODEL REFINEMENT | PHENIX | 1.21.1 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE |