7PTU

Structure of pentameric S-layer protein from Halofaerax volcanii


ELECTRON MICROSCOPY
Sample
Structure of pentameric S-layer protein csg
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsVitrobot options: Blot time 5 seconds, Blot force -10,1, Wait time 10 seconds, Drain time 0.5 seconds
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles382105
Reported Resolution (Å)3.87
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsThe final map (RELION3.1) was obtained from 382,105 particles and post-processed using a soft mask focused on the entire pentameric map yielding a glo ...The final map (RELION3.1) was obtained from 382,105 particles and post-processed using a soft mask focused on the entire pentameric map yielding a global resolution of 3.87 angstrom with resolution anisotropy from 3.49-8.11 angstrom from the central C5 axis near domains D1-D3 (well resolved) to the more flexible domains D4 (partially resolved) and D5-D6 (not resolved).
Refinement Type
Symmetry TypePOINT
Point SymmetryC5
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetBest Fit
Overall B Value179.68
Fitting Procedure
DetailsThe initial manual build of D1-D2 was performed independently using the csg pentameric cryo-EM map, which served as an additional validation of the ma ...The initial manual build of D1-D2 was performed independently using the csg pentameric cryo-EM map, which served as an additional validation of the manual building performed in the csg hexamer in the related deposition. The manual building exercise yielded a nearly identical result to the hexamer; thus, the final refined hexameric structures of D1-D2, along with D3-D4 were taken and fitted into the pentameric map (~3.87 angstrom resolution in D1-D3, lower in D4 which is partially resolved). Five copies of these D1-D4 were used for refinement and model building as for the hexamer, except D3 and D4 was restrained in position, due to steadily deteriorating resolution in this part of the map. D5-D6 were not resolved in the pentameric structure and were thus not included in the refinements. Model validation was performed in PHENIX and CCP-EM.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)53.9
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)4000
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 DetailsEPU software with faster acquisition mode AFIS (Aberration Free Image Shift).
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.0
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.1.13
MODEL FITTINGCoot0.9.2-pre
INITIAL EULER ASSIGNMENTRELION3.0
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19-4092
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.1773652Particles were initially picking using the Laplacian-of gaussian algorithm implemented in RELION3.0 (Zivanov et al., 2018). Particles were extracted in 8x down-sampled in 50x50 pixel boxes and classified using reference-free 2D classification inside RELION3.0.