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USP1 bound to ubiquitin conjugated to FANCD2 (focused refinement)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AY1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.014 f_angle_d 0.8032 f_chiral_restr 0.0553 f_bond_d 0.0099 f_plane_restr 0.0068
Sample USP1(C90S) bound to ubiquitin conjugated to FANCD2 Sample Components Ubiquitin-60S ribosomal protein L40 Ubiquitin carboxyl-terminal hydrolase 1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blotted for 3.0 secs before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 583484 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7AY1, 7AY1) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value 81.5 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING Coot 0.9.6 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.19
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6716868