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Structure of the yeast post-catalytic P complex spliceosome at 2.3 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EXN
Sample Yeast post-catalytic P complex spliceosome
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 209005 Reported Resolution (Å) 2.31 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6EXN) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details After fixing in ISOLDE, the model was refined in phenix.real_space_refine with the following non-default flags:
refinement {
run = *minimization_ ... After fixing in ISOLDE, the model was refined in phenix.real_space_refine with the following non-default flags:
refinement {
run = *minimization_global rigid_body local_grid_search morphing simulated_annealing *adp
}
reference_model {
enabled = True
use_starting_model_as_reference = True
fix_outliers = False
strict_rotamer_matching = True
}
pdb_interpretation {
reference_coordinate_restraints {
enabled = True
exclude_outliers = False
top_out = True
}
automatic_linking {
link_metals = True
}
peptide_link {
restrain_rama_outliers = False
restrain_rama_allowed = False
}
ramachandran_plot_restraints {
enabled = False
}
}
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1300 Maximum Defocus (nm) 3100 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.3 INITIAL EULER ASSIGNMENT RELION 5.0 FINAL EULER ASSIGNMENT RELION 5.0 CLASSIFICATION RELION 5.0 RECONSTRUCTION RELION 5.0 MODEL REFINEMENT ISOLDE 1.7 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1820457