5FOJ
Cryo electron microscopy structure of Grapevine Fanleaf Virus complex with Nanobody
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.331 |
f_angle_d | 0.825 |
f_chiral_restr | 0.052 |
f_bond_d | 0.009 |
f_plane_restr | 0.006 |
Sample |
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Grapevine fanleaf virus |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK III |
Cryogen Name | ETHANE |
Sample Vitrification Details | VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | |
Reported Resolution (Å) | 2.8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3246. (DEPOSITION ID: 14064). |
Refinement Type | |
Symmetry Type | |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (4V5T) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Initial atomic model building was done by a rigid body fitting, followed by extensive manual model building in Coot and real space refinement of the a ... |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 600 |
Maximum Defocus (nm) | 6000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 120000 |
Calibrated Magnification | 127272 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Cs-corrected microscope |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | UCSF Chimera | |
CTF CORRECTION | IMAGIC | |
RECONSTRUCTION | IMAGIC | |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY |