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2.12 A cryo-EM structure of Mycobacterium tuberculosis Ferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QD8
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 24.4262 f_angle_d 1.0927 f_chiral_restr 0.0696 f_bond_d 0.0171 f_plane_restr 0.0094
Sample Mycobacterium tuberculosis ferritin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 163568 Reported Resolution (Å) 2.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry O
Map-Model Fitting and Refinement Id 1 (3QD8) Refinement Space REAL Refinement Protocol OTHER Refinement Target Correlation coefficient Overall B Value 28.1 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 1400 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 130000 Calibrated Magnification 76757 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Basic direct alignments were done as well as astigmatism and coma alignment using AutoCTF
EM Software Task Software Package Version IMAGE ACQUISITION EPU 2.6.1 CTF CORRECTION Gctf 1.06 MODEL FITTING Coot 0.9.4 MODEL REFINEMENT PHENIX 1.18.2 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 249563