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Cryo-EM structure of S. Mansoni p97 bound to compound 739
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.606 f_angle_d 0.497 f_chiral_restr 0.041 f_bond_d 0.005 f_plane_restr 0.005
Sample Hexamer of p97 conjugated to inhibitor 739
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 101602 Reported Resolution (Å) 3.06 Resolution Method FSC 0.143 CUT-OFF Other Details Non-uniform refinement with C6 symmetry applied, with global and CTF refinements. Unsharpened map was used for modeling Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 (9P00) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details Apo structure was docked as initial model, then went through multiple rounds of manual fitting in coot and refinement in Phenix.
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2200 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 SerialEM CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2812039 Template pick with templates generated used the CB-5083-bound map