8C8L

ELECTRON MICROSCOPY

Sample

Nitrosopumilus maritimus S-layer

Specimen Preperation
Sample Aggregation State 2D ARRAY
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name NITROGEN
Sample Vitrification Details absorption for 60 sec and blotted for 5 sec with blot force -10
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 354860
Reported Resolution (Å) 2.71
Resolution Method FSC 0.143 CUT-OFF
Other Details Per-particle defocus, anisotropy magnification, and higher-order aberrations were refined inside RELION3.1, followed by three rounds of focused 3D auto refinement. Bayesian particle polishing was performed subsequently in a 640x640 pixel2 box followed by auto-refinement and symmetry relaxation. The final map was obtained from 354,860 particles and post-processed using a soft mask focused on the central hexamer, yielding a global resolution of 2.7 angstrom according to the Fourier shell correlation criterion between two independently refined half-maps at a threshold value at 0.143, and local resolution up to 2.5 angstrom
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space RECIPROCAL
Refinement Protocol AB INITIO MODEL
Refinement Target Best Fit
Overall B Value 41.4
Fitting Procedure ?
Details ?
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 48.5
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 2000
Maximum Defocus (nm) 5000
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 81000
Calibrated Magnification 81000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION Topaz 0.2.5
PARTICLE SELECTION RELION ?
IMAGE ACQUISITION EPU ?
CTF CORRECTION CTFFIND 4.1.13
MODEL FITTING Coot 0.9.2-pre
MODEL REFINEMENT PHENIX 1.19-4092
MODEL REFINEMENT REFMAC ?
INITIAL EULER ASSIGNMENT RELION 3.1
FINAL EULER ASSIGNMENT RELION 3.1
CLASSIFICATION RELION 3.1
RECONSTRUCTION RELION 3.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included.