ELECTRON MICROSCOPY

Sample

Pseudomonas phage phi6

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 13291
Reported Resolution (Å) 4.0
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 RIGID BODY FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B main-chains and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 0.73
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI POLARA 300
Minimum Defocus (nm) ?
Maximum Defocus (nm) 300
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model OTHER
Nominal Magnification 160000
Calibrated Magnification 37037
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION ETHAN 1.2
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION CTFFIND 3
CTF CORRECTION RELION 1.3
MODEL FITTING Coot 0.8.7
INITIAL EULER ASSIGNMENT RELION 1.3
FINAL EULER ASSIGNMENT RELION 1.3
CLASSIFICATION RELION 1.3
RECONSTRUCTION RELION 1.3
MODEL REFINEMENT Coot 0.8.7
MODEL REFINEMENT PHENIX 1.10.1_2155
MODEL FITTING Coot 0.8.7
MODEL REFINEMENT Coot 0.8.7
MODEL REFINEMENT PHENIX 1.10.1_2155
MODEL FITTING Coot 0.8.7
MODEL REFINEMENT Coot 0.8.7
MODEL REFINEMENT PHENIX 1.10.1_2155
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?