Figure 4. The σ^A Y217 may stack on the T₋₁₁(t) base orphaned by the flipped out A₋₁₁(nt) base.

(A) Synthetic oligonucleotides used for us-fork (−11 bp) crystallization. The numbers above the sequence denote the DNA position with respect to the transcription start site (+1). The DNA sequence is derived from the full con promoter (Gaal et al., 2001). The −35 and −10 (Pribnow box) elements are shaded yellow, the extended −10 element (Keilty and Rosenberg, 1987) purple. The nt-strand DNA (top strand) is colored dark grey; the t-strand DNA (bottom strand), light grey; the RNA transcript, red. (B) The T₋₁₁(t) base orphaned by the flipped out A₋₁₁(nt) stacks on σ^A Y217 in the us-fork (−11 bp) structure. The 4.6 Å-resolution electron density map (contoured at 0.7σ) is shown (grey mesh). Also superimposed is the simulated annealing omit map (green mesh, F_o − F_c, contoured at 3σ), calculated from a model where σ^A Y217 was mutated to Ala and the T₋₁₁(t) nucleotide was deleted.

DOI: http://dx.doi.org/10.7554/eLife.08504.013

Figure 4—figure supplement 1. Data and model quality for us-fork (−11 bp) complex.

Plots relating data quality with model quality at 4.6 Å-resolution) using the Pearson correlation coefficient (CC) analysis described by Karplus and Diederichs (2012). CC1/2 (red squares) was determined from the unmerged diffraction data randomly divided in half. Since CC1/2 underestimates the information content of the data (since it's calculated by dividing the dataset in half), CC* was calculated from an analytical relation to estimate the information content of the full data (Karplus and Diederichs, 2012). CC* provides a statistic that assesses data quality as well and also allows direct comparison of crystallographic model quality and data quality on the same scale through CC_work and CC_free, the standard and cross-validated correlations of the experimental intensities with the intensities calculated from the refined model. A CC_work/CC_free smaller than CC* indicates that the model does not account for all of the signal in the data, meaning it is not overfit. Plotted also are the standard <I>/σI for the diffraction data, as well as the R_work/R_free for the refined models.

DOI: http://dx.doi.org/10.7554/eLife.08504.014