Table 1.
Crystallographic Data and Refinement
| Data Collection | Native | AMPPNP | Mn2+ | AMPPNP-Mn2+ |
|---|---|---|---|---|
| Wavelength (Å) | 0.91841 | 0.91841 | 1.87856 | 1.87856 |
| Temperature (K) | 100 | 100 | 100 | 100 |
| Space Group | P212121 | P212121 | P212121 | P212121 |
| Unit Cell (Å) a, b, c | 58.7, 61.8, 100.2 | 59.0, 62.2, 97.9 | 58.9, 61.8, 101.5 | 58.9, 62.0, 100.6 |
| Resolution (Å) | 30.0-1.95 | 50.0-2.05 | 50.0-2.20 | 20.0-2.30 |
| (1.98-1.95)a | (2.09-2.05) | (2.24-2.20) | (2.36-2.30) | |
| Reflections | ||||
| Unique | 26982 (1269) | 22576 (1094) | 35224 (1513)b | 31058 (1968)b |
| Completeness (%) | 98.4 (94.7) | 97.7 (97.4) | 96.9 (84.4) | 98.2 (83.8) |
| Redundancy | 6.7 (6.1) | 5.2 (4.9) | 4.7 (2.7) | 4.5 (2.7) |
| I/σ(I) | 29.0 (1.9) | 15.9 (2.3) | 11.3 (1.3) | 14.4 (2.2) |
| Rsym(I) c | 3.6 (68.4) | 5.7 (66.4) | 9.0 (56.8) | 6.3 (49.7) |
|
| ||||
| Refinement | ||||
|
| ||||
| Resolution (Å) | 30.0-2.00 | 30.0-2.10 | 30.0-2.20 | 20.0-2.30 |
| (2.05-2.00) | (2.15-2.10) | (2.26-2.20) | (2.36-2.30) | |
| Reflections | ||||
| Number | 24959 (1727) | 21153 (1516) | 18858 (1180) | 16714 (1046) |
| Completeness (%) | 98.6 (94.3) | 97.7 (96.6) | 97.0 (84.2) | 100.0 (100.0) |
| Test Set (%) | 5.1 | 5.1 | 5.1 | 5.0 |
| Rwork d | 19.6 (24.8) | 21.9 (29.7) | 21.0 (28.5) | 17.9 (20.9) |
| Rfree d | 24.1 (31.5) | 26.8 (29.6) | 27.0 (39.9) | 23.4 (30.9) |
| ESU (Å)e | 0.14 | 0.20 | 0.19 | 0.17 |
| Refined Atoms | ||||
| Protein | 2461 | 2446 | 2422 | 2430 |
| Water | 235 | 199 | 141 | 196 |
| Ligands | 19 | 31 | - | 32 |
| Mean B-Factors (Å2) | ||||
| Wilson | 30.4 | 33.7 | 35.1 | 51.1 |
| Protein | 38.0 | 46.1 | 35.6 | 43.1 |
| Water | 46.2 | 46.3 | 38.5 | 46.9 |
| Ligand | 65.5 | 63.5 | - | 54.2 |
| Ramachandran Plot (%) f | ||||
| Favored | 96.0 | 94.4 | 97.0 | 95.7 |
| Outliers | 1.0 | 1.0 | 0.7 | 1.0 |
| RMSDa Target Geometry | ||||
| Bond Lengths (Å) | 0.011 | 0.011 | 0.010 | 0.010 |
| Bond Angles (°) | 1.322 | 1.209 | 1.248 | 1.324 |
| RMSD B-Factors (Å2) | ||||
| Main Chain Bonds | 0.661 | 0.437 | 0.549 | 0.589 |
| Main Chain Angles | 1.064 | 0.741 | 0.942 | 1.033 |
| Side Chain Bonds | 1.554 | 1.099 | 1.316 | 1.523 |
| Side Chain Angles | 2.277 | 1.719 | 2.110 | 2.493 |
| PDB ID | XXXX | XXXX | XXXX | XXXX |
a
Data for the highest resolution shell in parentheses
b
Mn2+ and AMPPNP-Mn2+ data sets were processed without merging Friedel pairs
c
Rsym(I) = ∑hkl∑i∣Ii(hkl) - <I(hkl)>∣ / ∑hkl∑i∣Ii(hkl)∣; for n independent reflections and i observations of a given reflection; <I(hkl)> - average intensity of the i observations
d
R = ∑hkl∥Fobs∣ - ∣Fcalc∥ / ∑hkl∣Fobs∣; Rwork - hkl ∉ T; Rfree - hkl ∊ T; T test set
e
ESU - estimated overall coordinate error based on maximum likelihood
f
Calculated with MolProbity (http://molprobity.biochem.duke.edu/)
g
RMSD - root-mean-square deviation