8C8M | pdb_00008c8m

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

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.7
r_dihedral_angle_4_deg	22.089
r_long_range_B_refined	18.65
r_long_range_B_other	18.65
r_dihedral_angle_3_deg	13.952
r_scangle_other	12.227
r_mcangle_it	9.148
r_mcangle_other	9.148
r_scbond_it	7.869
r_scbond_other	7.868
r_dihedral_angle_1_deg	6.213
r_mcbond_it	6.2
r_mcbond_other	6.2
r_angle_other_deg	1.485
r_angle_refined_deg	1.475
r_chiral_restr	0.066
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001
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 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)	2.87
Resolution Method	OTHER
Other Details	Composite map between C2 and C6 symmetrised maps. Created with refmac5 and the reference models as cutoffs
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
Fitting Procedure
Details	Composite map between C2 and C6 created using refmac5

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	48.5

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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.	1971908	Initially, 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.