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BRCA1-A complex: Ubiquitin bound to BRE at the wrist site (focused 3D class)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model ModelArchive ma-yb0lm
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.297 f_angle_d 0.709 f_chiral_restr 0.042 f_plane_restr 0.011 f_bond_d 0.003
Sample BRCA1-A complex bound to Lys-63 linked polyubiquitin chains Sample Components BRCA1-A complex Lys-63 Polyubiquitin chain analog
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot time: 5 s
Blot Force: 0
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 114857 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Classification on the wrist ubiquitin Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1250 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 4 PARTICLE SELECTION Topaz 0.2.5a PARTICLE SELECTION crYOLO 1.9.9 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4 MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING Coot 0.9.8 MODEL REFINEMENT Servalcat MODEL REFINEMENT PHENIX 1.21 INITIAL EULER ASSIGNMENT cryoSPARC 4 FINAL EULER ASSIGNMENT cryoSPARC 4 CLASSIFICATION cryoSPARC 4 RECONSTRUCTION cryoSPARC 4
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION