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TFIID-containing RNA polymerase II pre-initiation complex in the presence of the +1 nucleosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.2471 f_angle_d 1.1676 f_chiral_restr 0.0633 f_plane_restr 0.0109 f_bond_d 0.0067
Sample TFIID-containing RNA polymerase II pre-initiation complex in the presence of the +1 nucleosome Sample Components General transcription factor IIH Mammalian RNA polymerase II Nucleosome (protein) Nucleosome (DNA) General transcription factor IIB Transcription initiation factor IID General transcription factor IIF General transcription factor IIA General transcription factor IIE
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 30253 Reported Resolution (Å) 8.5 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 FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.7.1 IMAGE ACQUISITION SerialEM 4.0 CTF CORRECTION cryoSPARC 4.7.1 MODEL FITTING UCSF ChimeraX 1.9 INITIAL EULER ASSIGNMENT cryoSPARC 4.7.1 FINAL EULER ASSIGNMENT RELION 5.0 RECONSTRUCTION RELION 5.0 MODEL REFINEMENT ISOLDE 1.9 MODEL REFINEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 12714020