Table 1. Data collection and structure refinement statistics.
| Dataset | 1 | 2 | 3 | 4 |
|---|---|---|---|---|
| Data collection | ||||
| Ligand | Mg2+-ATP | Alanine | Glycine | Serine |
| Space group | P212121 | P212121 | P41212 | P41212 |
| Unit cell, Å | 173.6, 73.9, 74.0 | 173.0, 73.9, 74.0 | 73.9, 172.9 | 74.1, 173.6 |
| Complexes per a.u. | 2 | 2 | 1 | 1 |
| Wavelength, Å | 0.97976 | 1.0332 | 0.82653 | 0.97976 |
| Resolution, Å | 50.0-2.15 | 50.0-2.08 | 50.0-2.23 | 50.0-2.48 |
| Unique reflections | 50,235 (5,064) | 56,944 (5,680) | 24,242 (2,365) | 17,803 (1,739) |
| Completeness, % | 94.8 (96.9) | 99.8 (99.9) | 99.7 (100.0) | 98.7 (99.8) |
| Redundancy | 4.7 (4.8) | 4.3 (3.4) | 5.4 (5.4) | 13.4 (14.0) |
| Rmerge,* % | 3.5 (25.0) | 8.0 (17.0) | 8.3 (44.4) | 10.9 (38.1) |
| 〈I/σ(I)〉 | 20.4 | 15.3 | 12.0 | 11.5 |
| Structure refinement† | ||||
| No. of reflections: work/free | 44,397/4,965 | 51,940/5,804 | 21,716/2,384 | 15,913/1,761 |
| No. of atoms: protein/water | 7,284/190 | 7,284/361 | 3,642/194 | 3,642/147 |
| Ligands/Mg | 62/6 | 12/0 | 5/0 | 7/0 |
| Rcryst‡/Rfree,§ % | 19.4/22.5 | 18.9/23.6 | 20.7/23.9 | 19.9/23.2 |
| rmsd bond lengths, Å/angles, ° | 0.01/1.056 | 0.01/1.092 | 0.0185/1.431 | 0.0185/1.257 |
| Ramachandran plot, % | ||||
| Favored | 80.0 | 89.2 | 88.7 | 79.1 |
| Allowed | 19.4 | 10.3 | 10.3 | 20.0 |
| Generous | 0.6 | 0.5 | 1.0 | 0.9 |
| Average B factor, Å2 | ||||
| Protein | 30.6/38.8¶ | 22.0/24.1 | 20.2 | 22.2 |
| Ligands | 33.9/38.9 | 19.0/22.8 | 24.4 | 26.9 |
| Ions | 35.4 | — | — | — |
| Water | 32.3 | 25.0 | 21.2 | 46.0 |
Highest-resolution shell information is shown in parentheses.
*
Rmerge = 100 × (Σh Σi| 〈I(h)〉 - I(h)i|)/Σh Σi I(h)i, where I(h)i is the ith observation of reflection h and 〈I(h)〉 is the mean intensity of all observations of reflection h.
†
All observed data were used for refinement.
‡
Crystallographic R-factor = 100 × (Σh‖ Fobs(h) | - | Fcalc(h) ‖)/Σh | Fobs(h) |, where Fobs(h) and Fcalc(h) are the observed structure factor amplitude and the structure factor amplitude calculated from the model, respectively.
§
The free R-factor was calculated by using 90% of the data.
¶
For the orthorhombic crystals, two values are shown for the two molecules in the asymmetric unit (a.u.).