5OXE
Structure of major capsid protein VP1 of Aeropyrum pernix bacilliform virus 1 APBV1
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.726 |
r_dihedral_angle_3_deg | 24.644 |
r_long_range_B_refined | 22.829 |
r_long_range_B_other | 22.828 |
r_scangle_other | 19.055 |
r_dihedral_angle_4_deg | 15.731 |
r_mcangle_it | 13.873 |
r_mcangle_other | 13.872 |
r_scbond_it | 11.654 |
r_scbond_other | 11.65 |
Sample |
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Aeropyrum pernix bacilliform virus 1 |
Specimen Preparation | |
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Sample Aggregation State | HELICAL ARRAY |
Vitrification Instrument | |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 94645 |
Reported Resolution (Å) | 3.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C5 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | |||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 1 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI POLARA 300 |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | 37037 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | CTFFIND | 3 |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | SPRING | |
FINAL EULER ASSIGNMENT | SPRING | |
RECONSTRUCTION | SPRING | |
MODEL REFINEMENT | REFMAC | |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 169316 | Overlapping segments extracted from helical particles |