8C8R

In situ structure of the Nitrosopumilus maritimus S-layer - Composite map between C2 and C6


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.263
f_angle_d0.458
f_chiral_restr0.043
f_plane_restr0.003
f_bond_d0.002
Sample
Nitrosopumilus maritimus S-layer
Specimen Preparation
Sample Aggregation StateCELL
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameNITROGEN
Sample Vitrification Detailsabsorption for 60 sec and blotted for 5 sec with blot force -10
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles108621
Reported Resolution (Å)3.5
Resolution MethodOTHER
Other DetailsComposite map between C2 and C6
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetBest Fit
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)2.96
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)2000
Maximum Defocus (nm)5000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification105000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
VOLUME SELECTIONRELION4.0.0
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND4.1.13
CTF CORRECTIONRELION4.0.0
MODEL FITTINGCoot0.9.2-pre
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION4.0.0
CLASSIFICATIONRELION4.0.0
RECONSTRUCTIONRELION4.0.0
MODEL REFINEMENTPHENIX1.19-4092
MODEL REFINEMENTREFMAC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONPseudoSubtomograms as described in Zivanov 2022 (https://elifesciences.org/articles/83724)1971908Initially, side views of S-layer sheets were first manually picked along the edge of the lattice using the helical picking tab in RELION while setting the helical rise to 60 angstrom. Top and tilted views were manually picked at the central hexameric axis. Manually picked particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification inside RELION-3.1. Class averages centered at a hexameric axis were used to automatically pick particles inside RELION-3.1. Automatically picked particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification. Particle coordinates belonging to class averages centered at the hexameric axis were used to train TOPAZ in 5x downsampled micrographs with the neural network architecture conv127. For the final reconstruction, particles were picked using TOPAZ and the previously trained neural network above. Additionally, top, bottom, and side views were picked using the reference-based autopicker inside RELION-3.1, which TOPAZ did not readily identify. Particles were extracted in 4x downsampled 128x128 pixel2 boxes and classified using reference-free 2D classification inside RELION-3.1. Particles belonging to class averages centered at the hexameric axis were combined, and particles within 30 angstrom were removed to prevent duplication after alignment. All resulting particles were then re-extracted in 4x downsampled 128x128 pixel2 boxes.