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Cryo-EM structure of BCL6 bound to BI-3802
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MW2
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.5229 f_angle_d 1.0961 f_chiral_restr 0.057 f_bond_d 0.0123 f_plane_restr 0.0056
Sample B-cell lymphoma 6 protein (BCL6) filament
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details 4 ul sample applied twice, blotted 1.3s each time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 112048 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details as implemented in Relion Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5MW2) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details Real_space_refine: global minimization, rigid body and adp refinement with target restraints.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 63.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) -1000 Maximum Defocus (nm) -2500 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 Data collection in counting mode, using multi shot scheme (4 holes per stage position, 2 shots per hole)
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND CTF CORRECTION RELION MODEL FITTING Coot 0.89 MODEL REFINEMENT PHENIX 1.17 INITIAL EULER ASSIGNMENT RELION 3.0 FINAL EULER ASSIGNMENT RELION 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION RELION 3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Standard CTF correction in relion, based on parameters estimated by CTFFIND4 1610413 particles picked with crYOLO