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MS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IZM
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.3544 f_angle_d 0.4807 f_chiral_restr 0.0454 f_plane_restr 0.0043 f_bond_d 0.0023
Sample Escherichia phage MS2 capsid protein
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 239460 Reported Resolution (Å) 1.74 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (2IZM) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 54.58
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2000 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.21.1_5286
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 348343