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Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVD
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.345 f_angle_d 0.778 f_chiral_restr 0.043 f_bond_d 0.008 f_plane_restr 0.005
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 149479 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D4
Map-Model Fitting and Refinement Id 1 (1SVD) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 94.7 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 6000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION emClarity MODEL FITTING Coot FINAL EULER ASSIGNMENT emClarity RECONSTRUCTION emClarity MODEL REFINEMENT UCSF Chimera MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION