Table 2.
X-ray crystallography data collection and refinement statistics
| Inhibitor-free | pS9 | pS9-AlF3 | LRP6 c-motif | LRP6 e-motif | |
|---|---|---|---|---|---|
| PDB code | 4NM0 | 4NM3 | 4NU1 | 4NM5 | 4NM7 |
| Data collection* | |||||
| Space group | P6122 | P6122 | P6122 | P6122 | P6122 |
| Unit cell lengths a, c (Å) | 81.3, 280.8 | 81.0, 281.1 | 81.0, 280.5 | 81.7, 280.9 | 82.0, 280.3 |
| Beamline | SSRL 11-1 | SSRL 11-1 | APS 23-ID-B | SSRL 12-2 | SSRL 12-2 |
| Wavelength (Å) | 1.033 | 1.033 | 1.033 | 1.00 | 1.00 |
| Resolution range (Å) | 39.1–2.50 | 39.0–2.10 | 46.8–2.50 | 39.2–2.30 | 39.4–2.30 |
| (last shell) | (2.60–2.50) | (2.16–2.10) | (2.60–2.50) | (2.38–2.30) | (2.38–2.30) |
| Unique reflections | 20,069 | 33,093 | 19,922 | 25,685 | 25,932 |
| CC1/2† | 0.999 (0.726) | 1.00 (0.673) | 0.999 (0.814) | 0.999 (0.459) | 1.00 (0.485) |
| Rmerge‡ | 0.106 (1.74) | 0.100 (4.88) | 0.303 (6.772) | 0.141 (3.63) | 0.136 (4.31) |
| <I>/<σI> | 18.4 (1.2) | 24.5 (0.8) | 13.0 (0.7) | 18.9 (1.0) | 17.8 (0.9) |
| Completeness (%) | 100 (99.9) | 99.9 (99.7) | 100 (100) | 99.7 (99.6) | 100 (100) |
| Multiplicity | 9.6 (9.9) | 18.6 (17.9) | 21.0 (21.6) | 18.9 (18.1) | 18.7 (18.2) |
| Refinement | |||||
| No. reflections work/test set | 19,958/979 | 32,924/1658 | 19,823/974 | 25,608/1283 | 25,838/1292 |
| Rwork/Rfree§ | 0.191/0.240 | 0.194/0.242 | 0.191/0.245 | 0.183/0.232 | 0.183/0.234 |
| Number of atoms | |||||
| GSK-3 | 2780 | 2885 | 2862 | 2850 | 2858 |
| Axin | 165 | 153 | 149 | 155 | 155 |
| LrpC/E peptide | – | – | – | 44 | 44 |
| ADP | 27 | 27 | 27 | 27 | 27 |
| Mg2+ | 2 | 2 | 2 | 2 | 2 |
| Cl− | 1 | 1 | – | 1 | 1 |
| Glycerol | 30 | 24 | 12 | 24 | 18 |
| DTT | 8 | 8 | – | – | 8 |
| AlF3 | – | – | 4 | – | – |
| NO3− | – | – | 4 | – | – |
| Water | 164 | 197 | 98 | 121 | 106 |
| B-factors (Å2) | |||||
| GSK-3 | 52.6 | 55.0 | 75.1 | 69.7 | 69.7 |
| Axin | 59.5 | 54.0 | 78.1 | 75.2 | 77.8 |
| LrpC/E peptide | – | – | – | 101 | 100 |
| ADP | 65.3 | 50.3 | 57.5 | 72.2 | 56.5 |
| Mg2+ | 88.5 | 53.8 | 57.6 | 86.4 | 69.6 |
| Cl− | 77.1 | 71.1 | – | 90.9 | 96.8 |
| Glycerol | 65.2 | 79.4 | 93.1 | 94.6 | 97.2 |
| DTT | 99.3 | 102 | – | – | 131 |
| AlF3 | – | – | 83.6 | – | – |
| NO3− | – | – | 100.8 | – | – |
| Water | 46.4 | 52.3 | 61.1 | 64.3 | 64.6 |
| Rmsd | |||||
| Bond lengths (Å) | 0.003 | 0.005 | 0.003 | 0.002 | 0.004 |
| Bond angles (°) | 0.63 | 0.91 | 0.63 | 0.63 | 0.76 |
| Ramachandran plot (%)¶ | |||||
| Favored regions | 96.5 | 96.9 | 96.1 | 95.6 | 95.8 |
| Additional allowed regions | 3.5 | 3.1 | 3.9 | 3.9 | 4.2 |
| Outliers | 0 | 0 | 0.5 | 0.5 | 0 |
*
Values in parentheses are for highest-resolution shell. Rmsd, root mean square deviation.
†
As defined in Aimless (Evans and Murshudov, 2013).
‡
Rmerge = ΣhΣI|II(h)–< I(h) > |/ΣhΣI(h), where II(h) is the Ith measurement of reflection h, and < I(h) > is the weighted mean of all measurements of h.
§
R = Σh|Fobs(h)–Fcalc(h)|/Σh|Fobs(h)|. Rwork and Rfree were calculated using the working and test reflection sets, respectively.
¶
As defined in MolProbity (Chen et al., 2010).