6FYX | pdb_00006fyx

Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.856
r_dihedral_angle_3_deg19.177
r_dihedral_angle_1_deg17.192
r_dihedral_angle_4_deg12.642
r_long_range_B_refined12.563
r_mcangle_it5.089
r_mcbond_it2.78
r_scbond_it2.436
r_angle_refined_deg1.139
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.856
r_dihedral_angle_3_deg19.177
r_dihedral_angle_1_deg17.192
r_dihedral_angle_4_deg12.642
r_long_range_B_refined12.563
r_mcangle_it5.089
r_mcbond_it2.78
r_scbond_it2.436
r_angle_refined_deg1.139
r_chiral_restr0.112
r_bond_refined_d0.006
r_gen_planes_refined0.005
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
Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)
Sample Components
Ribosome
tRNA
Initiation factors
Initialtion factors
mRNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles74772
Reported Resolution (Å)3.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement TargetFSC
Overall B Value66
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)1500
Maximum Defocus (nm)3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification78000
Calibrated Magnification104478
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
PARTICLE SELECTIONEMAN
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera1.1
MODEL FITTINGCoot0.8
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTREFMAC5.8
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION706713