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USP1 bound to KSQ-4279 and ubiquitin conjugated to FANCD2 (focused refinement)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZH4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.186 f_angle_d 0.541 f_chiral_restr 0.037 f_plane_restr 0.004 f_bond_d 0.003
Sample USP1 BOUND TO KSQ-4279 AND UBIQUITIN CONJUGATED TO FANCD2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 89396 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7ZH4) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value 97.9 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC PARTICLE SELECTION Topaz CTF CORRECTION cryoSPARC MODEL FITTING Coot MODEL FITTING ISOLDE INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.20
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION