6EMK

Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined47.64
r_dihedral_angle_2_deg40.828
r_dihedral_angle_3_deg23.376
r_mcangle_it19.394
r_dihedral_angle_4_deg16.619
r_scbond_it11.153
r_dihedral_angle_1_deg10.876
r_mcbond_it10.668
r_angle_refined_deg2.024
r_chiral_restr0.153
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined47.64
r_dihedral_angle_2_deg40.828
r_dihedral_angle_3_deg23.376
r_mcangle_it19.394
r_dihedral_angle_4_deg16.619
r_scbond_it11.153
r_dihedral_angle_1_deg10.876
r_mcbond_it10.668
r_angle_refined_deg2.024
r_chiral_restr0.153
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details2 - 3 sec blotting
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles16190
Reported Resolution (Å)7.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Number of Particles10663
Reported Resolution (Å)8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (5FVM)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)5047
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM3.6
CTF CORRECTIONCTFFIND4
MODEL FITTINGCoot0.8.8
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
RECONSTRUCTIONRELION1.4
PARTICLE SELECTIONEMAN2
CTF CORRECTIONCTFFIND4
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTREFMAC5.8.0158
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION350000
PHASE FLIPPING AND AMPLITUDE CORRECTION200000