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Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BGD
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 49.736 r_long_range_B_other 49.735 r_scangle_other 36.329 r_dihedral_angle_2_deg 35.002 r_mcangle_it 33.984 r_mcangle_other 33.983 r_scbond_it 21.114 r_mcbond_it 21.107 r_mcbond_other 21.099 r_scbond_other 21.098
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 49.736 r_long_range_B_other 49.735 r_scangle_other 36.329 r_dihedral_angle_2_deg 35.002 r_mcangle_it 33.984 r_mcangle_other 33.983 r_scbond_it 21.114 r_mcbond_it 21.107 r_mcbond_other 21.099 r_scbond_other 21.098 r_dihedral_angle_3_deg 17.557 r_dihedral_angle_4_deg 11.677 r_dihedral_angle_1_deg 9.782 r_angle_refined_deg 1.301 r_angle_other_deg 0.96 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Specimen Preparation Sample Aggregation State PARTICLE
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 140155 Reported Resolution (Å) 4.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (4BGD, 4BGD) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 38
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 3500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 81000 Calibrated Magnification 35714 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION IMAGE ACQUISITION DigitalMicrograph CTF CORRECTION CTFFIND 4 MODEL FITTING Coot 0.8.3 MODEL REFINEMENT REFMAC 5.8 INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION CLASSIFICATION RELION RECONSTRUCTION RELION
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 473827