Table 2.
Data collection and refinement statistics
| WT E1p (Mn-ThDP) | S1-E1p (Mg-ThDP) | Phospho-S1-E1p (apo) | Phospho-S1-E1p (Mn-ThDP) | Y89F-α E1p (apo)e | |
|---|---|---|---|---|---|
| PDB code | 3EXE | 3EXF | 3EXG | 3EXH | 3EXI |
| Data collectiona | |||||
| Space group | P21 | P21 | P1 | C2 | P3221 |
| No. of E1p heterotetramers in the asymmetric unit | 2 | 2 | 8 | 2 | 0.5 (one heterodimer) |
| Unit cell | |||||
| a (Å) | 103.57 | 103.39 | 119.28 | 154.38 | 257.06 |
| b (Å) | 129.62 | 129.67 | 128.29 | 154.38 | 115.61 |
| c (Å) | 124.30 | 144.95 | 228.41 | 82.95 | 127.59 |
| α (°) | 90 | 90 | 90.14 | 90 | 90 |
| β (°) | 92.48 | 109.16 | 90.05 | 90 | 113.64 |
| γ (°) | 90 | 90 | 90.02 | 120 | 90 |
| Wavelength (Å) | 0.98 | 0.98 | 0.98 | 1.54 (Cu-Kα) | 0.98 |
| Resolution (Å) | 1.98 | 3.0 | 3.0 | 2.45 | 2.20 |
| Unique reflections | 225065 | 72201 | 263005 | 123888 | 57582 |
| Completeness (%) | 99.6 (99.0) | 99.8 (98.2) | 98.4 (98.0) | 98.1 (96.6) | 99.5 (99.5) |
| R-merge (%)b | 10.7 (55.1) | 14.6 (56.0) | 8.0 (53.5) | 15.5 (69.3) | 3.4 (39.9) |
| <I>/<σ(I)> | 13.3 (2.3) | 10.7 (2.6) | 10.3 (1.7) | 14.2 (2.8) | 33.0 (2.0) |
| Multiplicity | 4.9 (4.8) | 3.7 (3.4) | 2.1 (1.9) | 6.7 (6.5) | 6.6 (6.5) |
| Refinementa | |||||
| No. reflections (Work/Test) | 213690/11272 | 68497/3624 | 249289/13221 | 117572/6182 | 55098/1511 |
| No. atoms (Mean B value (Å2)) | |||||
| Protein | 21379 (17.7) | 21386 (21.6) | 83323 (55.7) | 5106 (49.2) | 21081 (18.8) |
| Solvents | 2316 (26.5) | 9 (6.9) | 0 | 318 (51.0) | 792 (19.0) |
| ThDP | 104 (11.4) | 104 (25.4) | 0 | 0 | 104 (17.7) |
| Metal and other | 32 (32.4) | 8 (32.8) | 16 (75.3) | 3 (65.7) | 58 (41.3) |
| R-work (%)c | 15.8 (20.1) | 18.4 (23.9) | 18.9 (29.5) | 16.5 (23.4) | 18.7 (28.1) |
| R-free (%)c | 20.6 (26.9) | 26.2 (35.8) | 25.3 (37.4) | 21.0 (28.5) | 22.5 (34.8) |
| R.m.s.d | |||||
| Bond length (Å) | 0.021 | 0.021 | 0.019 | 0.020 | 0.020 |
| Bond angle (°) | 1.761 | 2.044 | 1.883 | 1.733 | 1.842 |
| Ramachandran plot | |||||
| Most favored (%) | 96.5 | 90.2 | 92.1 | 96.1 | 96.3 |
| Allowed (%) | 2.2 | 6.8 | 5.7 | 2.8 | 2.5 |
| Disallowed (%) | 1.3 | 3.0 d | 2.2 d | 1.1 | 1.2 |
a
Values in parentheses refer to data in the highest resolution shell unless otherwise indicated.
b
R-merge = Σhkl Σj | Ij - <I> | / Σhkl Σj Ij, where <I> is the mean intensity of j observations from a reflection hkl and its symmetry equivalents.
c
R-work = Σhkl| |Fobs| − k|Fcalc| | / Σhkl |Fobs|. R-free = R-work for 5 % of reflections that were omitted from refinement.
d
The higher numbers result from the lower resolution (3.0 Å) of these structures than the others.
e
This crystal contains a complex of Y89F-α E1p with SBD, but SBD is not visible and excluded from the model.