Extended Data Fig. 4: Assessment of SWIM criteria.

(a-h) Assessment of the SWIM criteria on ~89,000 randomly sampled positions in the solvent shell (1.8–3.5 Å away from RNA that has a Q-score > 0.6 indicating high reliability of the RNA model) in the (a,c,e,g) 2.2 and (b,d,f,h) 2.3 Å maps. The distribution of (a-d) Q-score in each half-map, (e-f) Q-score in full map, and (g-h) map density-value are plotted. Cutoff values used for SWIM in this study are labeled with a gray dotted line (0.70 Q-score in full and half maps and 5σ above map mean value). The percent of randomly sampled solvent shell positions above these thresholds are labeled black. Then combining the criteria, the red number reports the number of positions that pass all the SWIM criteria. Our analysis showed that the SWIM criteria are stringent; only 0.6% of positions in the solvent shell of the maps pass all SWIM criteria. (i) The SWIM criteria are systematically varied, the number of waters identified in each map, the number of consensus waters between the two-map and the F1-score between the set of waters identified in the two maps are reported. (j-k) Distribution of Q-scores for SWIM-modeled water and Mg²⁺ ions. Expected Q-score at resolution for water and ion labeled as gray dashed line and the SWIM imposed Q-score threshold is labeled as a black dashed line. (l-m) As in J-K, but the water and Mg²⁺ ions are split by the number of interacting (<3.5 Å) RNA atoms. A trend shows an increase in Q-score with more interacting atoms but the trend is not statistically significant (linear regression, two-sided t = 1.826, p = 0.067). (n-o) Distribution of distances between water and Mg²⁺ ion and nearest atom. Thresholds used by SWIM are labeled as a black dashed line.