8C8M

In vitro structure of the Nitrosopumilus maritimus S-layer - Composite map between two and six-fold symmetrised


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.7
r_dihedral_angle_4_deg22.089
r_long_range_B_refined18.65
r_long_range_B_other18.65
r_dihedral_angle_3_deg13.952
r_scangle_other12.227
r_mcangle_it9.148
r_mcangle_other9.148
r_scbond_it7.869
r_scbond_other7.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.7
r_dihedral_angle_4_deg22.089
r_long_range_B_refined18.65
r_long_range_B_other18.65
r_dihedral_angle_3_deg13.952
r_scangle_other12.227
r_mcangle_it9.148
r_mcangle_other9.148
r_scbond_it7.869
r_scbond_other7.868
r_dihedral_angle_1_deg6.213
r_mcbond_it6.2
r_mcbond_other6.2
r_angle_other_deg1.485
r_angle_refined_deg1.475
r_chiral_restr0.066
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Nitrosopumilus maritimus S-layer
Specimen Preparation
Sample Aggregation State2D ARRAY
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 MethodSINGLE PARTICLE
Number of Particles354860
Reported Resolution (Å)2.87
Resolution MethodOTHER
Other DetailsComposite map between C2 and C6 symmetrised maps. Created with refmac5 and the reference models as cutoffs
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetBest Fit
Overall B Value
Fitting Procedure
DetailsComposite map between C2 and C6 created using refmac5
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)48.5
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 Magnification81000
Calibrated Magnification81000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONTopaz0.2.5
PARTICLE SELECTIONRELION
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.1.13
MODEL FITTINGCoot0.9.2-pre
MODEL REFINEMENTPHENIX1.19-4092
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONRELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included.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.