5LWG
Israeli acute paralysis virus heated to 63 degree - full particle
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.299 |
r_dihedral_angle_3_deg | 10.211 |
r_long_range_B_refined | 9.705 |
r_long_range_B_other | 9.705 |
r_dihedral_angle_4_deg | 8.062 |
r_dihedral_angle_1_deg | 7.454 |
r_mcangle_it | 4.188 |
r_mcangle_other | 4.188 |
r_scangle_other | 3.411 |
r_mcbond_it | 2.274 |
Sample |
---|
Israeli acute paralysis virus |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 9614 |
Reported Resolution (Å) | 3.2 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | initial rigid body fit was done by Chimera, then the model was refined using realspace refinement in Phenix and finaly reciprocal refined in REFMAC. |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 21 |
Imaging Experiment | 1 |
---|---|
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 | 75000 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | EMAN | 2.11 |
IMAGE ACQUISITION | EPU | 2 |
CTF CORRECTION | CTFFIND | 4 |
CTF CORRECTION | RELION | |
MODEL FITTING | UCSF Chimera | 1.11 |
INITIAL EULER ASSIGNMENT | RELION | 1.4 |
FINAL EULER ASSIGNMENT | RELION | 1.4 |
CLASSIFICATION | RELION | 1.4 |
RECONSTRUCTION | RELION | 1.4 |
MODEL REFINEMENT | PHENIX | 1.10.1 |
MODEL REFINEMENT | REFMAC | 5.8.0155 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |