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Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FVM
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 47.64 r_dihedral_angle_2_deg 40.828 r_dihedral_angle_3_deg 23.376 r_mcangle_it 19.394 r_dihedral_angle_4_deg 16.619 r_scbond_it 11.153 r_dihedral_angle_1_deg 10.876 r_mcbond_it 10.668 r_angle_refined_deg 2.024 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 47.64 r_dihedral_angle_2_deg 40.828 r_dihedral_angle_3_deg 23.376 r_mcangle_it 19.394 r_dihedral_angle_4_deg 16.619 r_scbond_it 11.153 r_dihedral_angle_1_deg 10.876 r_mcbond_it 10.668 r_angle_refined_deg 2.024 r_chiral_restr 0.153 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Target of rapamycin protein complex 2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 2 - 3 sec blotting
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 16190 Reported Resolution (Å) 7.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 10663 Reported Resolution (Å) 8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2 Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (5FVM) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 50 47
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3500 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM 3.6 CTF CORRECTION CTFFIND 4 MODEL FITTING Coot 0.8.8 INITIAL EULER ASSIGNMENT RELION 1.4 FINAL EULER ASSIGNMENT RELION 1.4 RECONSTRUCTION RELION 1.4 PARTICLE SELECTION EMAN2 CTF CORRECTION CTFFIND 4 INITIAL EULER ASSIGNMENT RELION 1.4 FINAL EULER ASSIGNMENT RELION 1.4 RECONSTRUCTION RELION 1.4 MODEL REFINEMENT REFMAC 5.8.0158
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 350000 PHASE FLIPPING AND AMPLITUDE CORRECTION 200000