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Structure of thioferritin exhibiting iron mineral nucleation, from Pyrococcus furiosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7STW
Sample Thioferritin dodecamer with loaded ferroxidase centers and no mineral core.
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 1619884 Reported Resolution (Å) 1.91 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry T
Map-Model Fitting and Refinement Id 1 (7STW) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value 75.5 Fitting Procedure Details Model was fit to map using ChimeraX fitmap, and then refined in PHENIX
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 55
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 600 Maximum Defocus (nm) 1600 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 57000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5 PARTICLE SELECTION crYOLO IMAGE ACQUISITION SerialEM 4.1 CTF CORRECTION cryoSPARC 4.5 MODEL FITTING UCSF ChimeraX 1.8 INITIAL EULER ASSIGNMENT cryoSPARC 4.5 FINAL EULER ASSIGNMENT cryoSPARC 4.5 CLASSIFICATION cryoSPARC 4.5 RECONSTRUCTION cryoSPARC 4.5 MODEL REFINEMENT PHENIX 1.21
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1742467