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Cryo-EM structure of S. Mansoni p97 bound to ATPgS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9P00
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.917 f_angle_d 0.42 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.003
Sample Hexamer of p97 bound to 2 copies of ATPgS-Mg in each chain
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 665490 Reported Resolution (Å) 2.2 Resolution Method FSC 0.143 CUT-OFF Other Details Homogenous refinement with C6 symmetry, global and local CTF refinements. DeepEMhancer sharpened map was used for modeling. Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 (9P00) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details Initial fitting done in ChimeraX using apo structure, then manually built using ISODLE and coot. Refined in Phenix.
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) 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 MODEL FITTING ISOLDE INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.20.1_4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1681589 Template picking using templates generated from CB-5083 bound map.