From: Structure of the stationary phase survival protein YuiC from B.subtilis
Crystal | +NAG (truncated K32-E218) | Apo (P73-E218) | +anhydro (R52-K217) |
PDB CODE | 4WJT | 4WLI | 4WLK |
Data collection | Â | Â | Â |
Wavelength (Ã…) | 0.9795 | 0.9200 | 0.9795 |
Space group | R3:H (146) (Hexagonal Cell) | C2221 (20) | R3:H (146) (Hexagonal Cell) |
Cell dimensions | Â | Â | Â |
  a, b, c (Å) | 145.5, 145.5, 37.8 | 50.0, 117.3, 61.0 | 147.2, 147.2, 37.9 |
 α, β, γ (°) | 90, 90, 120 | 90, 90, 90 | 90, 90, 120 |
Resolution (Å)a | 36.37–1.21 (1.23–1.21) | 30.8–1.76 (1.79–1.76) | 42.50–2.03 (2.08–2.03) |
Total number of reflections a | 290513 (14071) | 132867 (7892) | 74023 (5113) |
Number of unique reflections a | 89967 (4420) | 18150 (1026) | 19631 (1439) |
Rmerge a | 0.043 (0.569) | 0.098 (0.745) | 0.122 (0.576) |
Rmeas a | 0.060 (0.792) | 0.114 (0.860) | 0.162 (0.764) |
Rpim a | 0.041 (0.549) | 0.057 (0.425) | 0.106 (0.497) |
CC (1/2) a | 0.998 (0.607) | 0.998 (0.771) | 0.983 (0.620) |
Solvent content (%) | 45.7 | 53.3 | 44.0 |
Molecule/asymmetric unit | 2 | 1 | 2 |
Wilson B-factor (Ã…2) | 14.4 | 17.3 | 21.4 |
I/σI a | 10.3 (2.4) | 13 (2.5) | 7.5 (2.2) |
Completeness (%)a | 98.8 (97.2) | 99.8 (99.6) | 99.4 (98.7) |
Redundancy a | 3.2 (3.2) | 7.3 (7.7) | 3.8 (3.6) |
Refinement | Â | Â | Â |
Resolution (Å)a | 36.39–1.21 (1.23–1.21) | 30.798–1.76 (1.85–1.76) | 42.51–2.03 (2.14–2.03) |
Reflection, working | 85213 | 18131 | 19628 |
Reflection, free | 4468 | 927 | 968 |
Rwork/Rfree (%) | 11.1/14.4 | 16.2/20.2 | 16.76/20.80 |
No of non-H atoms | 2815 | 1264 | 2506 |
 Protein | A: 1185 B: 1185 | 1120 | A: 1139 B: 1133 |
 Others | 45 (NAG) | 16 (EDO) | 56 (1,6-anhydro-disaccharide) |
 | 13 (Polypropylene glycol) |  |  |
 | 16 (DMSO) |  |  |
 Water | 371 | 128 | 178 |
B factors (Ã…2)b | 24.0 | 26.6 | 32.4 |
 Protein | A: 21.7 B: 21.6 | 25.5 | A: 33.1 B: 31.2 |
 Others | 20.3 (NAG) | 35.1 (EDO) | 28.0 (1,6-anhydro-disaccharide) |
 | 44.5 (Polypropylene glycol) |  |  |
 | 64.6 (DMSO) |  |  |
 Water | 37.0 | 35.05 | 36.839 |
Rmsds | Â | Â | Â |
 Bond lengths (Å) | 0.023 | 0.016 | 0.005 |
 Bond angles (°) | 2.2 | 1.495 | 0.990 |
Ramachandran plot | Â | Â | Â |
 Favoured (%) | 98.1 | 97.8 | 95.4 |
 Allowed (%) | 1.8 | 2.4 | 4.6 |
 Outliers (%) | 0 | 0 | 0 |