Table 1.
Data collection and refinement statistics
| DDX21‐AMPPNP‐U15 | DDX21‐ADP | DDX21‐AMP | DDX21‐apo | |
|---|---|---|---|---|
| PDB code | 6L5N | 6L5O | 6L5M | 6L5L |
| Data collection | ||||
| Space group | P21 | P21 | P21 | C2 |
| Unit cell a,b,c (Å) | 72.36, 89.23, 79.69 | 66.46, 43.83, 72.44 | 36.39, 219.07, 126.39 | 146.17, 46.63, 58.49 |
| α, β, γ [°] | 90 115.6 90 | 90 115.64 90 | 90 90.79 90 | 90 101.16 90 |
| Resolution range (Å) a) | 40.00–2.24 (2.36–2.24) | 43.83–1.80 (1.90–1.80) | 40.00–2.70 (2.85–2.70) | 36.15–3.10 (3.27–3.10) |
| Total reflections | 276183 (41221) | 139159 (19644) | 219751 (33408) | 26341 (3993) |
| Unique reflections | 43794 (6378) | 33164 (4904) | 51933 (7930) | 6479 (952) |
| Multiplicity | 6.3 (6.5) | 4.2 (4.0) | 4.2 (4.2) | 4.1 (4.2) |
| Completeness (%) | 99.7 (99.9) | 94.6 (96.1) | 95.8 (99.7) | 90.5 (92.1) |
| I/σ (I) | 11.6 (3.7) | 7.9 (2.3) | 6.4 (2.5) | 9.8 (4.5) |
| Wilson B‐factor | 28.57 | 13.86 | 30.36 | 56.23 |
| R merge b) | 0.091 (0.449) | 0.129 (0.673) | 0.209 (0.682) | 0.123 (0.325) |
| R meas c) | 0.109 (0.536) | 0.145 (0.765) | 0.239 (0.780) | 0.140 (0.370) |
| R pim d) | 0.059 (0.29) | 0.065 (0.354) | 0.113 (0.374) | 0.065 (0.172) |
| R sym e) | 0.091 (0.449) | 0.129 (0.673) | 0.209 (0.682) | 0.123 (0.325) |
| CC1/2 f) | 0.996 (0.853) | 0.994 (0.722) | 0.976 (0.774) | 0.988 (0.930) |
| Refinement statistics | ||||
| Resolution (Å) | 33.33–2.24 (2.32–2.24) | 36.91–1.80 (1.86–1.80) | 36.51–2.70 (2.72–2.70) | 34.12–3.10 (3.17–3.10) |
| Reflections used in refinement | 43766 (4376) | 33156 (3299) | 51895 (1038) | 6479 (382) |
| Reflections used for R free | 2106 (190) | 1713 (171) | 2580 (49) | 349 (22) |
| R work g) | 0.175 (0.224) | 0.175 (0.230) | 0.207 (0.258) | 0.191 (0.209) |
| R free h) | 0.233 (0.289) | 0.209 (0.286) | 0.257 (0.306) | 0.241 (0.268) |
| No. residues | 754 | 372 | 1830 | 368 |
| RMSD | ||||
| Bond lengths (Å) | 0.012 | 0.007 | 0.01 | 0.008 |
| Bond angles (Å) | 1.28 | 0.87 | 1.13 | 1.02 |
| Average B‐factor | 37.69 | 20.73 | 25.7 | 33.14 |
| Ramachandran favored (%) | 98.8 | 99.19 | 97.4 | 96.11 |
| Ramachandran allowed (%) | 1.2 | 0.81 | 2.1 | 3.61 |
| Ramachandran outliers (%) | 0 | 0 | 0.5 | 0.28 |
| No. atoms | ||||
| Protein or RNA | 6266 | 2969 | 14470 | 2889 |
| Ligands or ions | 96 | 34 | 115 | – |
| water | 158 | 148 | 58 | – |
| B‐factors | ||||
| Protein or RNA | 37.96 | 20.53 | 25.8 | 30.25 |
| Ligands or ions | 30.66 | 17.82 | 21.85 | – |
| Water | 31.29 | 25.32 | 8.89 | – |
Values in parentheses are for the highest resolution shell
R merge = ∑|(I i −<I>) |/∑|I|, where I i is the intensity of an individual reflection and is the average intensity of that reflection
R meas, redundancy‐independent (multiplicity‐weighted) R merge
R pim, precision‐indicating (multiplicity‐weighted) R merge
R sym = ∑|(I −<I>) |/∑|I|, where I is the observed intensity
CC1/2 is the correlation coefficient of the mean intensities between two random half‐sets of data
R work = ∑||F o| − |F c||/∑|F o|, where F o and F c are the observed and calculated structure factors for reflections, respectively
R free was calculated as R work using the 5% of reflections that were selected randomly and omitted from refinement.