ELECTRON MICROSCOPY

Sample

Rous sarcoma virus - Prague C

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details blot time= 2.5 s blot force= 0
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 20498
Reported Resolution (Å) 3.1
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol AB INITIO MODEL
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details The CANTD and CACTD of one CA monomer of pdb 3TIR were independently placed into the EM-density using the rigid body fitting option in UCSF Chimera. Subsequently the linker connecting the two CA domains was joined in Coot. To account for the different monomer-monomer interactions in the RSV CA pentamer, the monomers were replicated according to the inherent 5-fold symmetry of the map and an additional ring of CACTDs was rigid-body fitted into the EM-densities of the surrounding CA pentamers. A map segment (defined by a mask extending 3 Angstrom around the rigid body fitted model) was extracted, and real-space coordinate refinement against the EM-density was performed using Phenix. This was iterated with manual model building in Coot, similar as described previously. In brief, secondary structure restraints and non-crystallographic symmetry (NCS) restraints were applied throughout all refinements. Each Phenix iteration consisted of 5 macro cycles, in which simulated annealing was performed in every macro cycle. Atomic displacement parameter (ADP) refinement was per formed at the end of each iteration.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 50
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TECNAI ARCTICA
Minimum Defocus (nm) 800
Maximum Defocus (nm) 1500
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 63000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION ?
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION Gctf ?
CTF CORRECTION RELION ?
MODEL FITTING UCSF Chimera ?
INITIAL EULER ASSIGNMENT RELION ?
FINAL EULER ASSIGNMENT RELION ?
CLASSIFICATION RELION ?
RECONSTRUCTION RELION ?
MODEL REFINEMENT PHENIX ?
MODEL REFINEMENT Coot ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF estimation and correction was performed using GCTF in the RELION wrapper