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. S ...
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/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (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
EM Software
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
150599
2394 micrographs were taken, from which 374 particles were manually picked and 2D classified to generate templates for auto-picking. Two rounds of auto-picking and 2D classification resulted in 150599 extracted particles.
