TABLE 1.
Data collection and refinement statistics
| Data set | ObcA |
|||||
|---|---|---|---|---|---|---|
| Ligand-free | Oxaloacetate | C4-CoA adduct | Ligand-free |
|||
| Peak | Edge | Remote | ||||
| Crystal | Methylated SeMet | Native | Native | Methylated SeMet | Methylated SeMet | Methylated SeMet |
| Wavelength (Å) | 0.97935 | 0.97948 | 0.97948 | 0.97935 | 0.97957 | 0.97167 |
| Resolution (Å)a | 50–2.1 (2.18–2.10) | 50–2.0 (2.07–2.00) | 50–2.28 (2.36–2.28) | 50–2.8 (2.90–2.80) | 50–2.8 (2.90–2.80) | 50–2.8 (2.90–2.80) |
| Total reflections | 548,745 | 474,350 | 311,761 | 264,040 | 263,537 | 267,962 |
| Unique reflections | 40,015 | 49,954 | 33,093 | 19,639 | 19,631 | 19,912 |
| Multiplicity | 13.7 (14.5) | 9.5 (9.8) | 9.4 (9.4) | 13.4 (13.2) | 13.4 (13.2) | 13.5 (13.1) |
| R-merge (%) | 18.0 (59.3) | 12.1 (49.5) | 15.0 (94.9) | 13.1 (51.4) | 12.3 (50.4) | 13.5 (62.4) |
| Completeness (%) | 95.9 (99.8) | 96.2 (100) | 99.6 (98.8) | 99.8 (100) | 99.7 (100) | 99.9 (100) |
| Mean I/sigma (I) | 12.1 (5.0) | 13.3 (4.7) | 11.4 (2.8) | 21.4 (5.7) | 24.2 (6.1) | 22.2 (4.9) |
| Wilson B-factor | 27.65 | 30.56 | 32.93 | |||
| Space group | P43212 | P43212 | P43212 | P43212 | P43212 | P43212 |
| Unit cell (Å) | ||||||
| a = b, c | 173.5, 46.2 | 177.0, 47.8 | 174.6, 46.1 | 178.2, 48.2 | 178.2, 48.2 | 178.2, 48.2 |
| α = β = γ | 90 | 90 | 90 | 90 | 90 | 90 |
| Refinement | ||||||
| Rwork (%)b | 19.8 | 21.0 | 20.2 | |||
| Rfree (%)c | 23.7 | 24.6 | 23.5 | |||
| No. of atoms | 4270 | 4056 | 3937 | |||
| Macromolecules | 3867 | 3741 | 3731 | |||
| Ligands | 1 | 10 | 62 | |||
| Water | 402 | 305 | 144 | |||
| Protein residuesd | 498 | 484 | 483 | |||
| Root mean square (bonds) | 0.007 | 0.007 | 0.008 | |||
| Root mean square (angles) | 1.08 | 1.09 | 1.13 | |||
| Ramachandran favored (%) | 97 | 96 | 96 | |||
| Ramachandran outliers (%)e | 0 | 0 | 0.21 | |||
| Clashscore | 2.45 | 2.93 | 2.78 | |||
| Average B-factor | 29.8 | 35.5 | 32.4 | |||
| Macromolecules | 29.3 | 35.3 | 32.1 | |||
| Ligands | 19.1 | 30.5 | 50.0 | |||
| Solvent | 34.7 | 38.2 | 31.8 | |||
a The numbers in parentheses refer to data in the highest resolution shell.
b Rwork = Σ||Fobs| − k|Fcal||/Σ|Fobs|.
c Rfree is the same as Robs for a selected subset (10%) of the reflections that was not included in prior refinement calculations.
d Ordered residues: ligand-free structure (Thr2–Ile70 and Arg92–Arg95 and His101–Ile525), oxaloacetate bound structure (Thr2–Ile70 and Ala111–Ile525), and a C4-CoA adduct bound structure (Thr2–Ile70 and Ala110–Ala523).
e Two outliers identified in C4-CoA adduct bound complex: Ser358 and Gly450.