Cell - 8 September 2016

Figure S2. Med-PIC Targeted Refinement Strategy, Related toFigure 2
(A) Heterogeneity analysis with high-dose/defocus particle set using Relion 3D-classification routines and a relion initial model shows a well ordered central map
section (pol II-Head-Middle-core GTFs) flanked by two highly mobile domains (Tail and TFIIH-E). Particle subsets showing well aligned TFIIH-E density (green
dashed line) lacked Mediator Tail density whereas improved Tail alignment led to poor resolution of the TFIIH-E domain (red dashed line). The refinement of Med-
PIC containing TFIIH-E involved the alignment of low-dose/defocus particles using a reference and mask lacking the Tail module (DTail), whereas the complex
containing Tail was resolved by excluding TFIIH-E density (DTFIIH-E). The presence of pol II-core GTF density in both targeted refinement maps allowed for the
alignment and recombination of the full complex from the partial structures.
(B) Reconstruction of theDTail andDTFIIH-E partial maps. Details of the reconstruction ofDTail (left) andDTFIIH-E (right) partial complex maps by single-particle
cryo-EM. The resolution of the partial complex maps using the gold-standard Fourier shell cutoff (FSC = 0.143) is shown.