5LJ3 | pdb_00005lj3

Structure of the core of the yeast spliceosome immediately after branching


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.163
r_long_range_B_refined19.477
r_long_range_B_other19.477
r_dihedral_angle_3_deg18.101
r_dihedral_angle_4_deg13.285
r_dihedral_angle_1_deg9.412
r_scangle_other9.208
r_mcangle_it8.839
r_mcangle_other8.839
r_scbond_it5.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.163
r_long_range_B_refined19.477
r_long_range_B_other19.477
r_dihedral_angle_3_deg18.101
r_dihedral_angle_4_deg13.285
r_dihedral_angle_1_deg9.412
r_scangle_other9.208
r_mcangle_it8.839
r_mcangle_other8.839
r_scbond_it5.329
r_scbond_other5.329
r_mcbond_it4.931
r_mcbond_other4.93
r_angle_refined_deg1.252
r_angle_other_deg1.02
r_chiral_restr0.089
r_bond_refined_d0.007
r_gen_planes_refined0.005
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
Spliceosome immediately after branching
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details3 microlitres sample were applied to the grid, left for 30 seconds and then blotted for 2.5-3.0 seconds before plunging.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles93106
Reported Resolution (Å)3.8
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 Target
Overall B Value
Fitting Procedure
DetailsUsed secondary structure restraints generated in ProSMART and LibG.
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)2
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification35714
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
CTF CORRECTIONCTFFIND4
MODEL FITTINGCoot0.8.3
MODEL REFINEMENTREFMAC5.8
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION248000