Table 1 Data collection and refinement statistics.
TMD-Mg 2+ | TMD-Mn 2+ | TMD-Mn 2+ | TMD-Ca 2+ | |
|---|---|---|---|---|
Data collection | ||||
X-ray source | SPring-8 BL32XU | |||
Space group | P212121 | |||
Cell dimensions | ||||
a, b, c (Å) | 62.5, 70.2, 102.7 | 63.5, 70.7, 103.2 | 66.1, 70.1, 102,6 | 63.7, 70.0, 103.2 |
α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
Wavelength (Å) | 1.000 | 1.000 | 1.450 | 1.000 |
Resolution (Å) | 50–2.3 (2.42–2.3) | 50–2.2 (2.32–2.2) | 50–2.84 (2.89–2.84) | 50–3.2 (3.37–3.2) |
Rsym | 0.183 (1.697) | 0.157 (1.368) | 0.084 (0.41) | 0. 258 (0.916) |
I/σ(I) | 6.4 (0.75) | 9.8 (1.5) | 5 (2.17) | 6.75 (1.67) |
Completeness (%) | 96.4 (98.2) | 98.7 (100.0) | 97.6 (94.5) | 91.5 (90.6) |
Redundancy | 4.1 (3.9) | 7.34 (7.34) | 5.4 (3.4) | 5.0 (4.5) |
CC1/2 | 0.994 (0.246) | 0.998 (0.679) | 0.982 (0.649) | |
Refinement | ||||
Resolution (Å) | 50–2.3 | 50–2.2 | 50–3.2 | |
No. reflections | 19,947 | 23,956 | 7,464 | |
Rwork/Rfree | 0.224/0.263 | 0.224/0.240 | 0.247/0.285 | |
No. atoms | ||||
Protein | 2,660 | 2,683 | 2,608 | |
Ligand/ion | 1 | 4 | 2 | |
Lipid | 66 | 90 | ||
Water | 39 | 75 | ||
B-factors | ||||
Protein | 49.06 | 39.79 | 54.82 | |
Ligand/ion | 38.31 | 53.81 | 58.16 | |
Lipid | 63.55 | 54.80 | ||
Water | 42.76 | 40.70 | ||
Root mean squared deviations | ||||
Bond length (Å) | 0.003 | 0.015 | 0.003 | |
Bond angle (°) | 0.734 | 0.726 | 0.876 | |
