7VFF
Cryo-EM structure of Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6BEI |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.939 |
f_angle_d | 0.699 |
f_chiral_restr | 0.053 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Sample |
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Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation in its trimeric state |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details | 3 microliter sample volume was loaded onto a holey grid with additional graphene oxide film. 10 sec waiting time, 5 sec blotting time and blot force 0 ... |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 156813 |
Reported Resolution (Å) | 4.1 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C3 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6BEI) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TALOS ARCTICA |
Minimum Defocus (nm) | 600 |
Maximum Defocus (nm) | 1200 |
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 | 92000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.1.9 |
CTF CORRECTION | RELION | 3.1 |
MODEL FITTING | UCSF Chimera | 1.13.1 |
MODEL FITTING | Coot | 0.9.1 |
MODEL REFINEMENT | PHENIX | 1.18 |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 743834 |