5MPS

Structure of a spliceosome remodeled for exon ligation


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.32
r_long_range_B_refined19.018
r_long_range_B_other19.018
r_dihedral_angle_3_deg14.397
r_dihedral_angle_4_deg14.129
r_dihedral_angle_1_deg9.753
r_scangle_other9.749
r_mcangle_it9.58
r_mcangle_other9.58
r_mcbond_it5.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.32
r_long_range_B_refined19.018
r_long_range_B_other19.018
r_dihedral_angle_3_deg14.397
r_dihedral_angle_4_deg14.129
r_dihedral_angle_1_deg9.753
r_scangle_other9.749
r_mcangle_it9.58
r_mcangle_other9.58
r_mcbond_it5.467
r_mcbond_other5.467
r_scbond_it5.401
r_scbond_other5.401
r_angle_refined_deg1.287
r_angle_other_deg1.012
r_chiral_restr0.083
r_bond_refined_d0.008
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
Saccharomyces cerevisiae spliceosome. Complex C just after Prp16-mediated remodeling
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details3.5 microlitres sample were applied to the grid, left for 25 seconds and then blotted for 3.0-3.5 seconds before plunging.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles65824
Reported Resolution (Å)3.85
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetFourier Shell Correlation
Overall B Value330
Fitting Procedure
DetailsUsed secondary structure restraints generated in ProSMART and LibG.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (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)4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsGIF Quantum energy filter, 20 eV slit width
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
CTF CORRECTIONCTFFIND4
MODEL FITTINGCoot0.8.3
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 CORRECTION350000Selected initial particles automatically using C complex 2D class averages, low-pass filtered to 20 Angstrom for automatic particle picking.