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yeast core m6A Methyltransferase Complex (ycMTC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.57 r_lrange_other 22.569 r_dihedral_angle_6_deg 16.827 r_dihedral_angle_3_deg 14.876 r_scangle_it 13.657 r_scangle_other 13.657 r_mcangle_it 10.437 r_mcangle_other 10.437 r_scbond_it 7.886 r_scbond_other 7.885
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.57 r_lrange_other 22.569 r_dihedral_angle_6_deg 16.827 r_dihedral_angle_3_deg 14.876 r_scangle_it 13.657 r_scangle_other 13.657 r_mcangle_it 10.437 r_mcangle_other 10.437 r_scbond_it 7.886 r_scbond_other 7.885 r_dihedral_angle_2_deg 7.863 r_mcbond_it 6.264 r_mcbond_other 6.262 r_dihedral_angle_1_deg 5.681 r_angle_refined_deg 1.537 r_angle_other_deg 0.471 r_ncsr_local_group_1 0.241 r_ncsr_local_group_3 0.235 r_ncsr_local_group_2 0.208 r_nbd_refined 0.206 r_ncsr_local_group_4 0.199 r_ncsr_local_group_5 0.197 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.073 r_chiral_restr_other 0.073 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_bond_other_d
Sample yeast core m6A Methyltransferase Complex
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 236407 Reported Resolution (Å) 2.62 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 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 RELION 4.0 PARTICLE SELECTION Topaz 0.2.5 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.8 MODEL FITTING ISOLDE 1.8 INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0 MODEL REFINEMENT Servalcat 5.8 MODEL REFINEMENT REFMAC 5.8
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION