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RNA polymerase II bound to minimal Alu RNA right arm in the alternative conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OIK
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.059 f_angle_d 0.7465 f_chiral_restr 0.05 f_plane_restr 0.0104 f_bond_d 0.0039
Sample RNA polymerase II bound to Alu RNA minimal right arm Sample Components RNA polymerase II Alu RNA Minimal Right Arm
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 90778 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5OIK) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 39.56 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 41
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2200 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU 2.11 CTF CORRECTION CTFFIND 4.1.5 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL FITTING ISOLDE 1.6.0 MODEL FITTING Coot 0.9.6 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.20
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 704869