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Human complex II-BATS bound to membrane-attached Rab5a-GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RX9
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.46 f_angle_d 0.528 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Sample VPS34-CII-BATS bound to membrane-attached RAB5A-GTP (C19S, C63S, Q79L) on a LUV membrane
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK I Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 8441 Reported Resolution (Å) 9.88 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9RX9) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target cross-correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 2.99
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 2000 Maximum Defocus (nm) 5000 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 VOLUME SELECTION crYOLO 1.9.9 VOLUME SELECTION RELION 5.0 beta4-commit-dfea29 MODEL REFINEMENT PHENIX 1.21rc1_5156: CTF CORRECTION CTFFIND 4.1 CTF CORRECTION RELION 5.0 beta4-commit-dfea29 FINAL EULER ASSIGNMENT RELION 5.0 beta4-commit-dfea29 CLASSIFICATION RELION 5.0 beta4-commit-dfea29 RECONSTRUCTION RELION 5.0 beta4-commit-dfea29
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF estimated with CTFFIND-4.1 (wrapper in Relion5), then corrected during 3D refinement and CTF tomo refine in Relion5.