6ODM
Herpes simplex virus type 1 (HSV-1) portal vertex-adjacent capsid/CATC, asymmetric unit
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.6096 |
f_angle_d | 0.9211 |
f_chiral_restr | 0.052 |
f_plane_restr | 0.007 |
f_bond_d | 0.0048 |
Sample |
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Human herpesvirus 1 strain KOS |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | The sample was manually blotted and frozen with a homemade plunger. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 42857 |
Reported Resolution (Å) | 4.3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C5 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | 100 | ||||
Fitting Procedure | |||||
Details | Capsid and CATC atomic models from Dai & Zhou, Science 2018 (PDB-6CGR) were docked into the C5 portal vertex map (EMD-9860) and manually refined in Co ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 25 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
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 | 14000 |
Calibrated Magnification | 24271 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | EMAN | 1.09 |
IMAGE ACQUISITION | Leginon | |
CTF CORRECTION | CTFFIND | 3.0 |
CTF CORRECTION | RELION | 2.1 |
MODEL FITTING | Coot | 0.8.6.1 |
INITIAL EULER ASSIGNMENT | RELION | 2.1 |
FINAL EULER ASSIGNMENT | RELION | 2.1 |
RECONSTRUCTION | RELION | 2.1 |
MODEL REFINEMENT | PHENIX | 1.13 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 45445 |