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Structure of apo BRCA1-A complex in presence of K63-oligoUbATA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB D_1292147638
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.165 f_angle_d 0.668 f_chiral_restr 0.042 f_plane_restr 0.01 f_bond_d 0.003
Sample BRCA1-A complex without substrate in the active sites
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 279338 Reported Resolution (Å) 3.25 Resolution Method FSC 0.143 CUT-OFF Other Details Maasked resolution. For unmasked resolution see FSC plot in this deposition. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9SMN) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details Starting model was fitted with coot and refined with Phenix real space refine and Refmac Servalcat.
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) 800 Maximum Defocus (nm) 2200 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 81000 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 CTF CORRECTION cryoSPARC 4 MODEL FITTING Coot 0.9.8 MODEL REFINEMENT PHENIX 1.21.2 MODEL REFINEMENT Servalcat 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 647888 Clean particles.