Table 1.
Summary of data collection, phasing, and refinement statistics. Data for the highest resolution shell are given in parentheses. Ramachandran plot statistics were calculated by MOLPROBITY.
| PDB code | 3E4F (wt+citric acid) |
3IJW (wt+CoA) |
3KZL (H183G +AcCoA) |
3N0S (H183A +AcCoA) |
3N0M (H183G +AcCoA) |
|---|---|---|---|---|---|
| Crystal | |||||
| Space group | P212121 | P212121 | P21 | P21 | P212121 |
| Unit cell | a=36.3 Å | a=36.5 Å | a=71.9 Å | a=72.0 Å | a=36.8 Å |
| b=108.0 Å | b=110.6 Å | b=109.2 Å | b=109.4 Å | b=110.6 Å | |
| c=132.8 Å | c=132.9 Å | c=73.8 Å | c=74.0 Å | c=132.6 Å | |
| α=β=γ=90° | α=β=γ=90° | β=112.0° | β=111.9° | α=β=γ=90° | |
| Solvent content (%) | 44 | 46 | 45 | 46 | 46 |
| Matthews coefficient (Å3/Da) | 2.2 | 2.3 | 2.2 | 2.3 | 2.3 |
| No. of molecules in asymmetric unit | 2 | 2 | 4 | 4 | 2 |
| Data collection | |||||
| Diffraction protocol | SAD | MR | MR | MR | MR |
| Wavelength (Å) | 0.9793 | 0.9793 | 0.9792 | 0.9786 | 0.9792 |
| Resolution (Å) | 50.00–2.00 | 50.00–1.90 | 50.00–2.10 | 50.00–2.15 | 50.00–2.40 |
| The highest resolution shell (Å) | 2.03–2.00 | 1.93–1.90 | 2.14–2.10 | 2.19–2.15 | 2.44–2.40 |
| Unique reflections | 36337 | 44002 | 61626 | 57925 | 21408 |
| Redundancy | 8.1(8.1) | 7.2(6.2) | 4.0(2.8) | 3.3(2.8) | 3.9(3.9) |
| Completeness (%) | 100(100) | 99.7(99.2) | 98.9(87.8) | 99.1(95.9) | 97.5(96.6) |
| I/σ(I) | 38.2(4.5) | 28.4(3.3) | 18.1(2.80) | 16.0(1.9) | 23.1(2.1) |
| Rmerge (%)- Bijvoet pairs merged | 8.2(49.6) | 9.0(55.5) | 11.7(57.1) | 9.0(48.7) | 8.4(54.6) |
| SAD analysis | |||||
| No. of Se sites located/theoretical | 17/18 | - | - | - | - |
| FOMMLPHARE | 0.27 | - | - | - | - |
| FOMDM | 0.74 | - | - | - | - |
| Refinement | |||||
| Reflections used for refinement | 34404 | 41511 | 57645 | 54459 | 20256 |
| Reflections in Rfree set | 1806 | 2203 | 3081 | 2907 | 1094 |
| Rwork (%) | 17.2 | 18.8 | 18.0 | 17.4 | 21.2 |
| Rfree (%) | 22.6 | 23.1 | 23.2 | 22.8 | 25.8 |
| RMSD bond length (Å) | 0.017 | 0.022 | 0.014 | 0.021 | 0.017 |
| RMSD bond angles (°) | 1.7 | 1.7 | 1.5 | 1.7 | 1.6 |
| Number of protein atoms | 4082 | 4139 | 8172 | 8260 | 4095 |
| Number of water molecules | 293 | 336 | 455 | 374 | 43 |
| Average B factor (Å2) | 32.3 | 32.7 | 17.9 | 15.6 | 57.1 |
| Average B factor - protein (Å2) | 32.0 | 32.2 | 17.4 | 14.2 | 57.4 |
| Average B factor - waters (Å2) | 42.2 | 37.8 | 20.8 | 35.7 | 43.1 |
| Average B factor – ligands (Å2) | 51.8 | 39.0 | 30.6 | 33.4 | 50.3 |
| B from Wilson plot (Å2) | 27.3 | 28.4 | 27.8 | 31.6 | 54.1 |
| Ramachandran plot | |||||
| Favored regions (%) | 96.8 | 97.2 | 97.3 | 97.2 | 95.4 |
| Additional allowed regions (%) | 3.2 | 2.8 | 2.7 | 2.8 | 4.6 |