ELECTRON MICROSCOPY

Sample

ClpB, BAP form, double walker B mutant

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 230000
Reported Resolution (Å) 4.6
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Local correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details Initial models of the monomer were generated using MODELLER v9.17 with previously determined crystal structures of ClpB or ClpB domains as templates (PDB ids 4CIU, 1QVR, 4HSE and 4LJ9). The crystal structure of E. coli ClpB (4CIU) was used as a main template, the crystal structure of T. thermophilus (1QVR) was used to model positions of the NTD and the crystal structures of AAA1 and AAA2 of E. coli ClpB (4HSE and 4LJ9) were used to model the pore loops disordered in other crystal structures. Initial rigid body fitting of the monomers in the map was manually done in Chimera using the Fit-in-Map tool. iMODFIT was used for fitting involving large domain motions. FlexEM was then used for refinement of secondary structures and loops in the map. Quality and improvement of the fit was assessed with TEMPy using the Segment based Manders Overlap Coefficient (SMOC) scores and segment based cross correlation scores. Ridig body fitting of ATPgammaS (structure extracted from PDB id 3EIH) into the nucleotide biding sides was manually done in Chimera using the Fit-in-Map tool. The target map for fitting of ATPgammaS was the difference map between experimental map and map generated using the nucleotide-free protein model revealing nucleotide densities. A round of real-space refinement was performed in phenix using energy minimization to fix the model's geometry and clashes.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 1
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 3000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION Gautomatch ?
IMAGE ACQUISITION EPU ?
CTF CORRECTION CTFFIND 4
MODEL FITTING iMODFIT ?
MODEL FITTING Flex-EM ?
INITIAL EULER ASSIGNMENT RELION 2.0
FINAL EULER ASSIGNMENT RELION 2.0
CLASSIFICATION RELION 2.0
RECONSTRUCTION RELION 2.0
MODEL REFINEMENT PHENIX 1.11.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?