Table 2.
Data Collection and Refinement Statistics, Glycine-free VCII RNA, Mutants, and Cation Identification
| Crystal | Free | Mutation U69C |
Mutation G35C-C70G |
Soaked in 10 mM MnCl2 |
Soaked in 10 mM Tl-acetate |
Soaked in 10 mM BaCl2 |
|---|---|---|---|---|---|---|
|
| ||||||
| PDB ID | 3OX0 | 3OXB | 3OXD | 3OXE | 3OXM | 3OXJ |
| Data Collection | ||||||
|
| ||||||
| Space group | P3221 | P3221 | P3221 | P3221 | P3221 | P3221 |
| Cell dimensions a,b,c (Å) | 84.3, 84.3, 199.9 | 84.0, 84.0, 197.8 | 84.0, 84.0, 200.0 | 83.4, 83.4, 199.0 | 83.7, 83.7, 200.1 | 84.2, 84.2, 201.4 |
| Wavelength (Å) | 1.0809 | 1.0809 | 1.0750 | 1.5000 | 0.9763 | 1.5000 |
| Resolutiona | 20.00-3.05 (3.16-3.05) |
20.00-2.95 (3.06-2.95) |
20.00-3.00 (3.11-3.00) |
20.00-2.90 (3.00-2.90) |
20.00-2.95 (3.00-2.95) |
30.00-3.20 (3.31-3.20) |
| Rmerge (%)a | 5.2 (48.7) | 6.2 (54.2) | 7.4 (52.4) | 6.3 (56.4) | 6.7 (51.2) | 8.1 (54.3) |
| <I>/σ(I)a | 34.8 (3.9) | 55.5 (4.0) | 41.5 (5.2) | 31.3(3.0) | 47.7 (5.5) | 29.2 (3.1) |
| Completeness (%)a | 99.8 (99.9) | 99.7(99.8) | 99.8 (99.9) | 99.9 (100.0) | 100.0 (100.0) | 99.9 (100.0) |
| Unique reflectionsa | 16,320 (1,600) | 17,666 (1,719) | 16,953 (1,624) | 18,565(1,814) | 17,793 (881) | 14,230 (1,390) |
| Redundancy | 7.1 (7.3) | 16.5 (12.2) | 12.1 (12.5) | 5.3 (5.4) | 11.2 (11.5) | 5.2 (5.4) |
|
| ||||||
| Structure Refinement | ||||||
|
| ||||||
| Resolution (Å) | 20.00-3.05 | 20.00-2.95 | 20.00-3.00 | 20.00-2.90 | 20.00-2.95 | 20.00-.20 |
| Working set reflections | 15,445 | 16,755 | 16,063 | 17,579 | 16,839 | 13,482 |
| Test set reflections | 824 | 899 | 857 | 947 | 904 | 714 |
| Rfactor /Rfree (%)a | 20.7 / 24.0 | 19.8 / 22.1 | 19.6 / 21.4 | 20.1 / 21.9 | 20.0 / 22.5 | 19.4 / 22.4 |
|
| ||||||
| Number of Nonhydrogen Atoms | ||||||
|
| ||||||
| RNA | 3,807 | 3,785 | 3,785 | 3,807 | 3,807 | 3,790 |
| Glycine | 0 | 0 | 0 | 10 | 10 | 10 |
| Cations | 28 | 33 | 34 | 42 | 37 | 45 |
|
| ||||||
| Average B-factors(Å2) | ||||||
|
| ||||||
| RNA | 56.5 | 58.2 | 46.9 | 40.9 | 33.9 | 69.9 |
| Glycine | - | - | - | 40.3 | 35.0 | 66.6 |
| Cations | 65.8 | 79.3 | 69.0 | 84.0 | 73.0 | 123.5 |
|
| ||||||
| RMSD Values | ||||||
|
| ||||||
| Bond lengths (Å) | 0.005 | 0.005 | 0.005 | 0.005 | 0.005 | 0.005 |
| Bond angles (°) | 1.069 | 1.082 | 1.064 | 1.011 | 1.021 | 1.110 |
| Estimated coordinate errorb | 0.290 | 0.304 | 0.253 | 0.236 | 0.255 | 0.302 |
a
Values for the highest resolution shell are in parentheses.
b
Estimated coordinate error based on maximum likelihood was calculated with REFMAC (Murshudov et al., 1997).