Table 1.
Crystallographic statistics of YB-1 CSD in complex with RNA oligos
| CAUC (5YTV) | A2U (5YTS) | U3A (5YTX) | C4G (5YTT) | |
|---|---|---|---|---|
| Data collection | ||||
| Space group | P62 | P62 | P62 | P62 |
| Cell dimensions | ||||
| a, b, c (Å) | 66.3, 66.3, 35.2 | 65.7, 65.7, 37.0 | 66.5, 66.5, 33.6 | 66.2, 66.2, 36.0 |
| α, β, γ (degrees) | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 |
| Resolution (Å) | 30–1.70 (1.76–1.70)a | 50–1.77 (1.83–1.77) | 30–1.55 (1.61–1.55) | 50–1.60 (1.66–1.60) |
| Rmerge | 0.095 (0.327) | 0.083 (0.600) | 0.053 (0.609) | 0.070 (0.671) |
| I/σ(I) | 30.0 (6.8) | 30.7 (1.9) | 35.4 (2.2) | 26.6 (2.4) |
| Completeness (%) | 100.0 (100.0) | 99.0 (94.1) | 98.9 (98.9) | 96.4 (78.5) |
| Redundancy | 16.6 (12.3) | 7.3 (5.3) | 6.0 (5.0) | 9.2 (6.9) |
| Refinement | ||||
| Resolution (Å) | 30–1.7 | 30–1.77 | 30–1.55 | 30–1.60 |
| No. of reflections | 9,677 | 8,943 | 12,345 | 10,965 |
| Rwork/Rfree | 0.196/0.228 | 0.187/0.227 | 0.200/0.240 | 0.182/0.218 |
| No. of atoms | ||||
| Protein | 582 | 601 | 593 | 616 |
| RNA | 82 | 80 | 84 | 125 |
| Water | 52 | 57 | 50 | 62 |
| Mean B-factors (Å2) | ||||
| Protein | 25.4 | 28.4 | 32.1 | 21.5 |
| RNA | 41.6 | 44.5 | 60.2 | 47.5 |
| Water | 33.7 | 39.5 | 46.7 | 36.9 |
| Root mean square deviations | ||||
| Bond lengths (Å) | 0.007 | 0.006 | 0.006 | 0.007 |
| Bond angles (degrees) | 1.071 | 0.901 | 0.919 | 1.072 |
| Ramachandran plot | ||||
| Favored (%) | 100.0 | 94.7 | 100.0 | 100.0 |
| Allowed (%) | 0.0 | 5.3 | 0.0 | 0.0 |
| Outlier (%) | 0.0 | 0.0 | 0.0 | 0.0 |
a Numbers in parentheses are for the outer-resolution shell.