5Y88

Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.387
r_long_range_B_refined28.378
r_long_range_B_other28.378
r_scangle_other16.579
r_mcangle_it14.991
r_mcangle_other14.991
r_dihedral_angle_4_deg13.758
r_dihedral_angle_3_deg12.647
r_scbond_it9.818
r_scbond_other9.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.387
r_long_range_B_refined28.378
r_long_range_B_other28.378
r_scangle_other16.579
r_mcangle_it14.991
r_mcangle_other14.991
r_dihedral_angle_4_deg13.758
r_dihedral_angle_3_deg12.647
r_scbond_it9.818
r_scbond_other9.818
r_mcbond_it9.067
r_mcbond_other9.067
r_dihedral_angle_1_deg8.666
r_angle_refined_deg1.456
r_angle_other_deg0.96
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.008
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
S. cerevisiae intron lariat spliceosome (ILS)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles150363
Reported Resolution (Å)3.46
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)37.6
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONUCSFImage4
CTF CORRECTIONGctf
INITIAL EULER ASSIGNMENTRELION2.0
FINAL EULER ASSIGNMENTRELION2.0
CLASSIFICATIONRELION2.0
RECONSTRUCTIONRELION2.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION