Table 2 Data collection and refinement statistics
T-state MtbPYK | MtbPYK-OX | MtbPYK-OX/ATP/AMP | MtbPYK-OX/G6P | MtbPYK-OX/AMP/G6P | MtbPYK- OX/AMP/G6P (soak) | |
|---|---|---|---|---|---|---|
PDB ID | 5WRP | 5WS8 | 5WS9 | 5WSA | 5WSB | 5WSC |
Data collection | ||||||
Space group | P212121 | P31 | P31 | P31 | P31 | P31 |
Cell dimensions | ||||||
a, b, c (Å) | 90.76,129.48,243.98 | 127.01,127.01,144.65 | 127.19,127.19,144.92 | 125.42,125.42,144.19 | 125.63,125.63,144.51 | 124.37,124.37,144.19 |
α, β, γ (°) | 90.00,90.00,90.00 | 90.00,90.00,120.00 | 90.00,90.00,120.00 | 90.00,90.00,120.00 | 90.00,90.00,120.00 | 90.00,90.00,120.00 |
Solvent content (%) | 65 | 63 | 63 | 62 | 62 | 61 |
Resolution (Å) | 88.79–2.85 | 63.51–2.62 | 60.54–1.90 | 62.71–2.85 | 62.82–2.25 | 53.85–2.40 |
No. of reflections | 271,505 (15,837) | 432,224 (25,144) | 1,001,199 (43,594) | 333,176 (25,316) | 616,913 (15,502) | 541,318 (24,538) |
No. of unique reflections | 67,441 (4498) | 78,513 (4558) | 206,700 (10,249) | 59,240 (4587) | 120,301 (5497) | 97,539 (4826) |
Wilson B-factor (Å2) | 55.070 | 50.351 | 23.261 | 37.737 | 31.826 | 24.399 |
R merge (%) | 11.4 (92.7) | 9.4 (75.6) | 7.1 (44.6) | 10.3 (45.5) | 10.0 (89.9) | 17.4 (86.8) |
I/σI | 7.9 (1.1) | 10.6 (2.2) | 12.0 (3.0) | 13.7 (3.3) | 9.9 (1.4) | 8.3 (1.6) |
Completeness (%) | 99.4 (99.9) | 100.0 (100.0) | 100.0 (100.0) | 100.0 (100.0) | 99.3 (92.1) | 100.0 (99.9) |
Multiplicity | 4.0 (3.5) | 5.5 (5.5) | 4.8 (4.3) | 5.6 (5.5) | 5.1 (2.8) | 5.5 (5.1) |
Refinement | ||||||
Monomers in ASU | 4 | 4 | 4 | 4 | 4 | 4 |
No. of reflections | 63,878 | 74,461 | 195,933 | 56,202 | 114,312 | 92,706 |
R work/R free | 0.2056/0.2330 | 0.1734/0.2178 | 0.1968/0.2229 | 0.1509/0.1953 | 0.1870/0.2278 | 0.1793/0.2270 |
No. of non-H atoms | ||||||
Protein | 13549 | 14044 | 14211 | 14172 | 14172 | 14172 |
Water | 234 | 494 | 1440 | 172 | 410 | 335 |
Ligands | 20 | 28 | 269 | 112 | 195 | 195 |
Average B-factor (Å2) | ||||||
Protein | 76.0 | 70.2 | 36.3 | 43.6 | 37.4 | 28.2 |
Water | 55.8 | 57.7 | 43.4 | 24.3 | 27.2 | 22.1 |
Ligands | 76.8 | 65.9 | 47.4 | 32.8 | 31.1 | 23.4 |
AMP/G6P | N.A. | N.A. | 30.0 | 33.1 | 30.9 | 23.6 |
RMS deviations | ||||||
Bond lengths (Å) | 0.0123 | 0.0117 | 0.0121 | 0.0143 | 0.0119 | 0.0140 |
Bond angles (°) | 1.1760 | 1.1809 | 1.2636 | 1.3289 | 1.3243 | 1.5284 |
Ramachandran plots | ||||||
Favoured (%) | 97.1 | 96.7 | 98.3 | 97.2 | 97.3 | 97.8 |
Allowed (%) | 99.8 | 99.8 | 99.6 | 99.8 | 99.6 | 99.6 |
Number of outliers | 4 | 4 | 8 | 4 | 8 | 8 |
