EMD-6747 Experiments and Validation

RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS

Single particle reconstruction
Overview of EMD-6747
Sample name: RNA polymerase II elongation complex bound with Spt4/5 and TFIIS
Organisms: Komagataella pastoris, Yeast, synthetic construct, Komagataella phaffii (strain GS115 / ATCC 20864)
Fitted atomic model: 5xon

Map parameters

Recommended contour level: 0.067 (author)
Number of grid points: 180 × 180 × 180
Voxel size: 1.53 × 1.53 × 1.53 Å
Minimum density: -0.288
Maximum density: 0.503
Average density: 0.002
Standard deviation: 0.016

Sample information

Sample name: RNA polymerase II elongation complex bound with Spt4/5 and TFIIS
Ligands: ZINC ION, MAGNESIUM ION
Nucleic acids: RNA (30-MER), DNA (48-MER), DNA (48-MER)
Proteins: RNA polymerase II elongation complex bound with Spt4/5 and TFIIS, RNA polymerase II, Spt4/5 and TFIIS, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III, DNA-directed RNA polymerase subunit, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit, found in RNA polymerase complexes I, II, and III, General transcription elongation factor TFIIS, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: RELION
Number of particles: 682749

Fitting

Details: Model fitting was done with Chimera and Coot. Well-ordered regions were also refined with phenix.real_space_refine.

Imaging

Session
Microscope model: FEI TECNAI ARCTICA
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 50.0
Holder model: OTHER
Acquisition
Number of images: 3607

Specimen

Preparation
Specimen state: particle
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE