Table 1. Crystallographic data collection and structure refinement statistics.
| Ligand | none | phosphate (tRNA) | ATP | 2'-AMP | 3'-AMP | ATP | NADP+ |
|---|---|---|---|---|---|---|---|
| Data collection statistics | |||||||
| Space group | P21 | P1 | C2 | P4212 | P21 | C2 | C2 |
| Cell parameters | |||||||
| a (Å) | 63.39 | 54.73 | 101.95 | 108.07 | 63.41 | 102.15 | 86.74 |
| b (Å) | 88.32 | 63.52 | 73.33 | 108.07 | 88.35 | 73.47 | 91.62 |
| c (Å) | 73.84 | 67.37 | 77.49 | 72.64 | 73.97 | 77.61 | 120.61 |
| α (°) | 90 | 106.26 | 90 | 90 | 90 | 90 | 90 |
| β (°) | 115.01 | 106.14 | 128.54 | 90 | 114.95 | 128.34 | 102.32 |
| γ (°) | 90 | 103.06 | 90 | 90 | 90 | 90 | 90 |
| No. of molecules in ASU | 4 | 4 | 2 | 2 | 4 | 2 | 4 |
| Wavelength (Å) | 1.03 | 1.04 | 1.04 | 1.04 | 1.04 | 1.04 | 1.03 |
| High resolution (Å) | 2.10 | 2.80 | 2.10 | 2.46 | 2.75 | 1.80 | 1.70 |
| High-resolution shell (Å) | 2.15–2.10 | 2.88–2.80 | 2.15–2.10 | 2.52–2.46 | 2.82–2.75 | 1.85–1.80 | 1.74–1.70 |
| Unique reflections | 43063 (3154) | 18651 (1460) | 26124 (1890) | 15451 (613) | 19216 (1356) | 41617 (3088) | 100969 (7397) |
| Multiplicity | 3.81 (3.83) | 2.21 (2.20) | 3.81 (3.78) | 6.60 (2.58) | 3.80 (3.76) | 3.38 (3.33) | 3.80 (3.86) |
| Completeness (%) | 99.6 (99.8) | 95.7 (94.3) | 99.2 (99.2) | 95.4 (52.4) | 99.3 (97.8) | 99.2 (99.5) | 99.8 (99.8) |
| Rmerge | 0.076 (0.918) | 0.126 (0.942) | 0.075 (0.829) | 0.079 (0.621) | 0.092 (0.804) | 0.047 (1.061) | 0.053 (1.043) |
| Rmeas | 0.089 (1.067) | 0.171 (1.270) | 0.088 (0.967) | 0.086 (0.747) | 0.107 (0.939) | 0.056 (1.258) | 0.061 (1.211) |
| <I/σ(I)> | 11.93 (1.30) | 7.21 (1.02) | 14.16 (1.65) | 18.01 (1.51) | 14.11 (1.76) | 15.47 (1.31) | 13.92 (1.23) |
| CC½ (%) | 99.8 (58.1) | 97.8 (41.3) | 99.8 (64.8) | 99.9 (71.2) | 99.6 (62.9) | 99.9 (50.8) | 99.9 (61.9) |
| Wilson B (Å2) | 35.6 | 42.6 | 32.0 | 47.4 | 46.1 | 28.8 | 27.3 |
| Refinement statistics | |||||||
| Resolution range (Å) | 36.60–2.10 | 22.96–2.80 | 23.37–2.10 | 29.04–2.46 | 28.75–2.75 | 19.70–1.8 | 117.84–1.70 |
| High-resolution shell (Å) | 2.15–2.10 | 2.88–2.80 | 2.15–2.10 | 2.54–2.46 | 2.82–2.75 | 1.85–1.80 | 1.74–1.70 |
| Reflections in the working set | 40878 (2698) | 16784 (1279) | 24120 (1685) | 13888 (728) | 17272 (1183) | 39641 (2810) | 98860 (6928) |
| Reflections in the test set | 2153 (142) | 1859 (144) | 1997 (141) | 1544 (78) | 1922 (126) | 1975 (147) | 1998 (139) |
| R value (%) | 17.74 (27.52) | 21.77 (34.36) | 20.18 (26.83) | 19.70 (34.24) | 21.17 (31.25) | 17.06 (29.33) | 18.34 (38.32) |
| Rfree value (%) | 22.67 (29.43) | 25.80 (40.78) | 24.76 (32.97) | 25.28 (39.44) | 25.87 (38.53) | 20.35 (34.02) | 21.26 (41.66) |
| RMSD bond length (Å) | 0.004 | 0.003 | 0.008 | 0.005 | 0.003 | 0.019 | 0.007 |
| RMSD angle (°) | 0.981 | 0.705 | 1.148 | 0.937 | 0.830 | 1.834 | 1.321 |
| Atoms in ASU* | 11652 (5579) | 5490 | 2949 | 5771 (2854) | 5475 | 3322 (12) | 7048 |
| Protein atoms in ASU | 5561 | 5444 | 2721 | 2807 | 5449 | 2902 | 6059 |
| Ligand atoms in ASU | 3 | 25 | 31 | 47 | 23 | 99 | 351 |
| Water molecules in ASU | 509 | 21 | 197 | 63 | 3 | 279 | 638 |
| Mean B value (Å2) | 54.9 | 60.80 | 36.45 | 64.03 | 48.21 | 42.91 | 39.45 |
| Ramachandran plot | |||||||
| Favoured regions (%) | 99.26 | 99.40 | 97.88 | 98.25 | 97.74 | 99.72 | 98.63 |
| Allowed regions (%) | 0.59 | 0.60 | 2.12 | 1.75 | 1.36 | 0.28 | 1.09 |
| Outlier residues (%) | 0.15 | 0 | 0 | 0 | 0.90 | 0 | 0.27 |
| Clashscore | 2.42 | 3.93 | 5.09 | 2.46 | 5.02 | 12.07 | 8.46 |
| Rotamer outliers (%) | 0.87 | 1.79 | 6.07 | 3.03 | 0.89 | 1.33 | 2.23 |
| PDB entry | 5ldi | 5ldj | 5ldk | 5ldm | 5ldo | 5ldp | 5ldq |
* Number of riding hydrogen atoms is shown in parentheses.