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5'-lobe of the substrate-bound U11 snRNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9BV90-F1 in silico model AlphaFold AF-Q16560-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.0044 f_angle_d 0.7097 f_chiral_restr 0.0345 f_plane_restr 0.0051 f_bond_d 0.0029
Sample 5'-lobe of the substrate-bound U11 snRNP
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 52290 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correction coefficient Overall B Value 73.3 Fitting Procedure Details refinement is done in Phenix
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 41.73
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 1500 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Preliminary grid screening was performed on Glacios.
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.3.1 IMAGE ACQUISITION SerialEM MODEL FITTING UCSF ChimeraX 1.6.1 INITIAL EULER ASSIGNMENT cryoSPARC v4.3.1 FINAL EULER ASSIGNMENT cryoSPARC v4.3.1 CLASSIFICATION cryoSPARC v4.3.1 RECONSTRUCTION cryoSPARC v4.3.1 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 4494715 Topaz picking is performed with user-trained model