6TED
Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 8.948 |
f_angle_d | 1.342 |
f_chiral_restr | 0.083 |
f_bond_d | 0.025 |
f_plane_restr | 0.008 |
Sample |
---|
Complete EC* |
Sample Components |
Pig DNA/RNA polymerase subunits |
Human transcription factors and associated proteins |
DNA/RNA |
Transcription elongation factor SPT4 and SPT5 |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s. |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 446195 |
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 (6GMH, 4L1U, 6AFO) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | 115 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
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 | Warp | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | Warp | |
MODEL FITTING | UCSF Chimera | |
MODEL FITTING | NAMD | |
INITIAL EULER ASSIGNMENT | RELION | 3.0 |
FINAL EULER ASSIGNMENT | RELION | 3.0 |
RECONSTRUCTION | RELION | 3.0 |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 611983 |