6P4G | pdb_00006p4g

Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.686
r_dihedral_angle_3_deg13.868
r_dihedral_angle_4_deg13.629
r_long_range_B_refined10.709
r_long_range_B_other10.709
r_dihedral_angle_1_deg8.41
r_mcangle_it7.265
r_mcangle_other7.265
r_scangle_other6.355
r_mcbond_it4.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.686
r_dihedral_angle_3_deg13.868
r_dihedral_angle_4_deg13.629
r_long_range_B_refined10.709
r_long_range_B_other10.709
r_dihedral_angle_1_deg8.41
r_mcangle_it7.265
r_mcangle_other7.265
r_scangle_other6.355
r_mcbond_it4.288
r_mcbond_other4.287
r_scbond_it3.747
r_scbond_other3.747
r_angle_other_deg1.234
r_angle_refined_deg1.162
r_chiral_restr0.064
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot force = 3s Wait time = 15s Drain time = 0s Blot time = 2.5 to 3 s
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot force = 3s Wait time = 15s Drain time = 0s Blot time = 2.5 to 3 s
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles91056
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)42.1
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI F30
Minimum Defocus (nm)800
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.26
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification31000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatch
IMAGE ACQUISITIONLeginon
CTF CORRECTIONGctf
INITIAL EULER ASSIGNMENTRELION
FINAL EULER ASSIGNMENTRELION
CLASSIFICATIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1240275