Comparison between 2Fo−Fc and anomalous difference maps around a K+ with no first coordination shell. (A) 2Fo−Fc density pattern at 3.0 σ. The closest rRNA oxygen and nitrogen atoms are outside the first coordination shell of K+ (2.8–3.4 Å; Fig. 1B). (B) Extract of the 6QNR “in-house” diagnosis program output that lists the closest contact distances to the ion shown in A—the water molecule mentioned in the table and belonging to a Mg(H2O)62+ is not shown. (C) Four and three density patterns (four different crystals have been analyzed that differ from the one used to calculate the density maps shown in panel A) derived from the 6QNR anomalous diffraction data at the 3.351 (four data sets) and 3.542 Å (three data sets) wavelengths, respectively (Rozov et al. 2019). Note that for K+, f″ ≈ 4.0 e− and f″ ≈ 0.5 e− at the 3.351 and 3.542 Å wavelengths, respectively. Therefore, a K+ anomalous signal should be visible in the “A” data set but absent in the “B” data set. The fact that none of the anomalous difference densities overlap with the original assignment underlines the ambiguity of such data and the possibility that the four new and nonisomorphous crystals locally differ from the original crystal obtained 10 yr earlier in slightly different conditions even if similar crystallization protocols were used. Note the probable presence of an anomalous signal for a phosphorus atom in crystals 1, 2, and 4 as noted by Rozov et al. (f″ = 1.75 e− for P at a wavelength of 3.351 Å) and the presence of densities not directly linked to K+.
