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Cryo-EM structure of the ZBTB5 BTB domain filament
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 11.0416 f_angle_d 0.6763 f_chiral_restr 0.0393 f_plane_restr 0.0048 f_bond_d 0.0022
Sample ZBTB5 BTB domain filament
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C with 10 s pre-blot, 3 s blot, 3 s post-blot.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1352367 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 194 Fitting Procedure Details Real-space refinement without local grid search
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50.7
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2400 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 4.4.1 IMAGE ACQUISITION SerialEM 4.1b CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL FITTING ISOLDE 1.6.0 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1 MODEL REFINEMENT PHENIX 1.19.2-4158
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6344567