7QVX
Cryo-EM structure of coxsackievirus A6 altered particle
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5XS4 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.994 |
r_dihedral_angle_4_deg | 13.159 |
r_dihedral_angle_3_deg | 12.947 |
r_long_range_B_refined | 12.736 |
r_long_range_B_other | 12.736 |
r_dihedral_angle_1_deg | 5.539 |
r_scangle_other | 5.465 |
r_mcangle_it | 5.126 |
r_mcangle_other | 5.126 |
r_scbond_it | 3.273 |
Sample |
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Coxsackievirus A6 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 131286 |
Reported Resolution (Å) | 2.5 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (5XS4) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | 29 | ||||
Fitting Procedure | |||||
Details | iterative cycles of building - real space refinement - reciprocal space refinement |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 45 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 3000 |
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 | 75000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | |
IMAGE ACQUISITION | EPU | 1.12 |
CTF CORRECTION | Gctf | 1.06 |
MODEL FITTING | UCSF Chimera | |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
MODEL REFINEMENT | Coot | 0.9.5 |
MODEL REFINEMENT | PHENIX | 1.19.2 |
MODEL REFINEMENT | REFMAC | 5 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 211991 |