Table 2. X-ray data collection and refinement statistics.
| Se-Met StOFOR2 | Native StOFOR2 | StOFOR2 Pyruvate | StOFOR1 | |
|---|---|---|---|---|
| Data collection | ||||
| PDB entry | 5B46 | 5B47 | 5B48 | |
| Beamline | NW12A | BL5A | NW12A | BL5A |
| Wavelength (Å) | 0.9793 | 1.0000 | 1.0000 | 0.9780 |
| Space group | C2221 | C2221 | C2221 | P212121 |
| Unit cell (Å) | a = 100.6b = 204.0c = 126.0 | a = 101.9b = 205.0 = 127.0 | a = 100.7b = 203.7c = 126.0 | a = 75.2b = 145.9c = 170.1 |
| Resolution (Å)a | 50.00–2.50(2.54–2.50) | 50.00–2.10(2.14–2.10) | 50.00–2.20(1.99–2.20) | 50.00–2.50(2.59–2.50) |
| Total reflections | 674,899 | 574,608 | 478,719 | 281,054 |
| Unique reflections | 86,404 | 76,707 | 65,439 | 65171 |
| Completeness (%)a | 100.0 (100.0) | 98.7 (97.9) | 99.9 (100.0) | 99.2 (93.7) |
| Redundancya | 7.8 (7.8) | 7.5 (7.5) | 7.3 (7.1) | 4.3 (3.1) |
| Mean I/σ (I)a | 24.3 (3.2) | 30.3 (3.1) | 32.1 (3.0) | 27.0 (1.7) |
| CC 1/2 | (0.932) | —b | (0.882) | —b |
| Rmerge (%)a | 8.9 (61.6) | 7.3 (60.5) | 6.2 (66.6) | 5.8 (37.3) |
| Refinement | ||||
| Resolution (Å) | 33.93–2.10 | 36.17–2.20 | 98.93–2.50 | |
| No. of reflections | 72,834 | 61,011 | 61,283 | |
| R/Rfree (%) | 17.6/21.9 | 20.5/25.9 | 21.9/28.1 | |
| No. of atoms | 7,592 | 7,310 | 13,074 | |
| Protein chains | A, B | A, B | A–D | |
| Cofactors and ligands | TPP, Mg2+, [4Fe4S] | TPP, Mg2+, [4Fe4S] | 1-hydroxy propyl-TPP, Mg2+, [4Fe4S] (A) | |
| No. of solvents | 263 (water) | 191 (water) | 61 (water) | |
| Average B-factor (Å2) | ||||
| Protein atoms | 42.2 (A + B) | 53.1 (A + B) | 67.7 (A + B)67.7 (C + D) | |
| Cofactors and ligands | 50.3 (TPP-Mg2+)39.5 ([4Fe-4S]) | 102 (TPP-Mg2+)68.5 ([4Fe-4S]) 76.9 (pyruvate) | 58.0 (1-hydroxy-propyl-TPP-Mg2+) 60.8 ([4Fe-4S]) | |
| Waters | 40.3 | 47.2 | 52.4 | |
| RMSD from ideal values | ||||
| Bond length (Å) | 0.018 | 0.019 | 0.014 | |
| Bond angles (°) | 1.93 | 1.96 | 1.76 | |
| Ramachandran Plot (%) | ||||
| Favored | 97.3 | 96.1 | 93.8 | |
| Allowed | 2.3 | 3.6 | 4.7 | |
| Outlier | 0.4 | 0.3 | 1.5 | |
aThe numbers in parentheses indicate the highest resolution shell.
bThe dataset was processed by HKL-2000 of versions earlier than 2.3.2.