“…The four RNA fragments with sequences shown in Figure 1B were chemically synthesized and purified as described by Murray et al+ (1994)+ The MS2 coat protein was overexpressed in E. coli and the self-assembled, RNA-free protein capsids formed were purified according to Valegård et al+ (1986) and Mastico et al+ (1993)+ Crystals in the spacegroup R32, with cell dimensions a ϭ b ϭ 288+0 Å and c ϭ 653+0 Å, were grown from the MS2 coat protein capsids using the hanging drop technique under conditions described earlier (Valegård et al+, 1986)+ RNA fragments were added to the empty capsid crystals to a final concentration of 2 mg/mL (Valegård et al+, 1994;van den Worm et al+, 1998)+ Diffraction data for the Loop complex were collected at station 9+6 at the CLRC Daresbury Laboratory, United Kingdom+ The wavelength was 0+87 Å and the temperature 5 8C+ Data sets for the A-bulge, the F-bulge, and the Clamp complexes were collected at station ID2 at ESRF, Grenoble, France+ The wavelength was 1+00 Å and the temperature 10 8C+ In all cases, the oscillation angle was 0+58 and a MAR Research image plate detector was used+ The data sets for A-bulge, F-bulge, and Clamp complexes were processed and scaled using the HKL package (Otwinowski & Minor, 1996)+ Loop data was processed with Denzo (Otwinowski & Minor, 1996) and scaled using the CCP4 package (Collaborative Computational Project, 1994)+ Table 1 presents statistics from the scaling of the data for the four complexes+ Initial phases were obtained by molecular replacement using the model of the empty capsid of MS2 coat protein+ The phases were refined by cyclic averaging using the noncrystallographic symmetry and the program RAVE (Kleywegt & Jones, 1994)+ Models of Loop RNA and Clamp RNA complexes were built using the program O (Jones et al+, 1991)+ The program X-PLOR (Brünger, 1990) was used for positional refinement using the conjugate gradient-type minimization and for refinement of restrained temperature factors of the two models+ The values of occupancies for the RNA molecules were chosen to give temperature factors of the RNA atoms participating in hydrogen bonds to the protein in the same range as in earlier studies+ For the Loop model, the occupancies for both A/B and C/C binding RNA molecules were therefore set to 0+6 and for the Clamp model these values were set to 0+5+…”