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gp39 protein from Escherichia phage vB_EcoS_NBD2, unbent tubule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.0013 f_angle_d 0.579 f_chiral_restr 0.0466 f_plane_restr 0.0049 f_bond_d 0.003
Sample gp39 protein from Escherichia phage vB_EcoS_NBD2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 73243 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Indicated resolution is for the Focused map 1 used to obtain the composite map. Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 30
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 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) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU 3.0 CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX 1.7 MODEL REFINEMENT PHENIX 1.21.2_5419 RECONSTRUCTION cryoSPARC 4.7.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION