Table 1 Data collection, phasing and refinement statistics
Apo SeMet-RmlT | Apo RmlT/ HEPES | RmlT/ UDP-glucose | RmlT/TDP-rhamnose | RmlTD198A/TDP-rhamnose | RmlT/3-RboP | RmlT/4-RboP | |
|---|---|---|---|---|---|---|---|
PDB ID | 8BZ4 | 8BZ5 | 8BZ6 | 8BZ7 | 8BZ8 | 9GZJ | 9GZK |
Diffraction data | |||||||
Space group | P 21 21 21 | P 1 21 1 | P 1 21 1 | P 1 21 1 | P 1 21 1 | P 21 21 21 | P 1 21 1 |
Cell dimensions | |||||||
a, b, c (Å) | 83.4, 103.7, 178.4 | 82.1, 178.4, 92.2 | 85.5, 291.1, 89.8 | 87.0, 291.3, 92.4 | 87.4, 292.4, 93.1 | 83.2, 103.4, 178.6 | 86.3, 290.8, 91.0 |
α, β, γ (°) | 90.0, 90.0, 90.0 | 90.0, 93.5, 90.0 | 90.0, 100.1, 90.0 | 90.0, 100.4, 90.0 | 90.0, 100.5, 90.0 | 90.0, 90.0, 90.0 | 90.0, 100.2, 90.0 |
Resolution (Å) | 49.8–2.52 | 48.1–2.30 | 49.3–2.40 | 50.0–2.20 | 49.3–2.52 | 48.4–2.34 | 49.0–2.52 |
Rmergea | 0.210 (1.735) | 0.112 (1.295) | 0.103 (1.560) | 0.059 (1.087) | 0.113 (1.394) | 0.079 (1.363) | 0.071 (1.053) |
I / σIa | 9.8 (1.5) | 10.7 (1.4) | 12.2 (1.3) | 14.0 (1.2) | 12.9 (1.6) | 16.2 (1.2) | 13.2 (1.4) |
Completenessa (%) | 100 (100) | 99.2 (98.4) | 99.1 (97.7) | 99.8 (99.7) | 100 (100) | 99.9 (98.7) | 99.5 (99.8) |
Redundancya | 13.6 (13.3) | 7.0 (7.2) | 7.2 (7.3) | 3.8 (3.6) | 7.1 (7.1) | 6.6 (6.0) | 3.5 (3.5) |
Refinement | |||||||
Resolution (Å) | 49.8–2.52 | 48.1–2.30 | 44.2–2.40 | 50.0–2.20 | 45.8–2.52 | 41.6–2.34 | 42.9–2.52 |
No. reflections | 53,011 | 115,974 | 166,253 | 227,111 | 153,926 | 65,950 | 147,192 |
Rwork / Rfree | 0.219 / 0.251 | 0.193 / 0.220 | 0.195 / 0.235 | 0.187 / 0.215 | 0.191 / 0.228 | 0.192 / 0.226 | 0.198 / 0.232 |
Total No. atoms | 9,848 | 20,336 | 30,490 | 30,744 | 30,233 | 9,962 | 29,353 |
Total No. water molecules | 241 | 502 | 674 | 1,193 | 673 | 282 | 334 |
R.m.s deviations | |||||||
Bond lengths (Å) | 0.003 | 0.004 | 0.004 | 0.005 | 0.002 | 0.003 | 0.002 |
Bond angles (°) | 0.521 | 0.586 | 0.581 | 0.670 | 0.470 | 0.552 | 0.424 |
Ramachandran plot | |||||||
Favoured (%) | 95 | 96 | 96 | 97 | 97 | 96.58 | 95.69 |
Allowed (%) | 5 | 4 | 4 | 3 | 3 | 3.42 | 4.31 |
Outliers (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Ligand | – | – | UDP-glucose | TDP-rhamnose | TDP-rhamnose | 3-RboP | 4-RboP |
Molecules in the asymmetric unit | 2 | 4 | 6 | 6 | 6 | 2 | 6 |
Best defined chain(Mean RSRZ) | A (0.04) | B (0.03) | E (0.15) | A (0.12) | A, C, D (0.04) | A (−0.32) | A, C, D, E (−0.17) |
Residues NOT modelled (per chain) | A: M1-K17; B: M1-K20, E31-E33, G60-T65, K82-G90, G227-F234. | A: M1-N15, A228-S232; B: M1- K16, A228-F234; C: M1-N15; D: M1-K16; S87-W89; G227-S232. | All chains: M1-K17; B: also missing L623. | A: M1-K17, A228-S232; B: M1-K17, N230-F234; C: M1-K17, N230-G235; D: M1- K16, A228-G235; E and F: M1-K17, G227-F234. | A, C, D: M1-K17, N230-S232; B: M1-K17, A228-S232; E, F: M1-K17, G227-S233. | A: G0-N15; B: G0-D18, T30-G34, D58-Y66, K82-G90, G227-F234, L623. | A: G0-K16, A228-F234; B: G0-K17, A228-S232; C and D: G0-K17, G227-S233; E: G0-K17, G227-S231; F: G0-K17, T62-T75, A228-F234, L536-T545, L565-577, L596-V607, I619-L623. |
