Table 3.
Crystallographic data for LiAcs1 and CaAcs2 structures
| Sample |
LiAcs1 |
LiAcs1 |
LiAcs1 |
LiAcs1 |
LiAcs1 |
CaAcs2 |
|---|---|---|---|---|---|---|
| Ligand |
AMP-acetate/CoA |
AMP/CoA |
Ethyl-AMP |
AMP-K+/CoA |
Ethyl-AMP-P21 |
Amp-CoA |
| PDB code | (8SF3) | (8U2T) | (8U2R) | (8U2U) | (8U2S) | (8V4R) |
| Data collection | ||||||
| Unit cell parameters (Å,o) | a = 59.02 | a = 59.07 | a = 58.91 | a = 58.75 | a = 91.21 | a = b = 139.41 |
| b = 69.38 | b = 69.92 | b = 74.15 | b = 69.46 | b = 61.81 | c = 542.25 | |
| c = 151.62 | c = 150.72 | c = 151.05 | c = 149.38 | c = 134.81 | ||
| b = 92.98 | ||||||
| Space group | P212121 | P212121 | P212121 | P212121 | P21 | P6122 |
| Resolution (Å)a | 151.62–1.70 (1.74–1.70) | 49.49–1.65 (1.68–1.65) | 46.45–1.55 (1.58–1.55) | 74.69–1.97 (2.02–1.97) | 134.63–2.52 (2.59–2.52) | 49.46–2.70 (2.75–2.70) |
| Wavelength (Å) | 0.9795 | 0.9795 | 0.9795 | 0.9795 | 0.9795 | 0.9795 |
| Temperature (K) | 100 | 100 | 100 | 100 | 100 | 100 |
| Observed reflections | 898,647 | 1,022,350 | 1,288,859 | 583,642 | 272,635 | 1,734,018 |
| Unique reflections | 68,961 | 75,992 | 96,781 | 44,111 | 51,168 | 86,857 |
| <I/σ(I)>a | 12.3 (1.8) | 14.5 (1.9) | 16.0 (1.8) | 13.5 (1.6) | 9.3 (1.6) | 14.5 (1.7) |
| Completeness (%)a | 99.5 (98.5) | 100 (100) | 100 (100) | 99.9 (99.6) | 99.9 (100) | 100 (100) |
| Multiplicitya | 13.0 (13.6) | 13.5 (13.9) | 13.3 (13.6) | 7.0 (6.4) | 5.3 (5.6) | 20.0 (19.1) |
| Rmerge (%)ab | 12.8 (175.0) | 11.0 (173.1) | 8.4 (164.2) | 11.2 (161.4) | 13.7 (118.0) | 18.5 (235.2) |
| Rmeas (%)ad | 13.3 (181.7) | 11.5 (179.7) | 8.7 (170.6) | 11.7 (168.7) | 15.2 (129.9) | 18.9 (241.6) |
| Rpim (%)ad | 3.7 (48.8) | 3.1 (47.8) | 2.4 (46.0) | 3.2 (47.5) | 6.4 (53.7) | 4.2 (55.1) |
| CC1/2ae | 0.998 (0.693) | 0.999 (0.762) | 0.999 (0.654) | 0.999 (0.873) | 0.997 (0.596) | 0.999 (0.800) |
| Refinement | ||||||
| Resolution (Å)a | 44.95–1.70 | 45.12–1.65 | 23.84–1.55 | 40.47–1.97 | 91.08–2.52 | 49.46–2.70 |
| Reflections (working/test)a | 65,452/3405 | 72,074/3795 | 91,862/4819 | 64,534/2196 | 48,521/2575 | 82,259/4353 |
| Rfactor/Rfree (%)ac | 15.0/18.7 | 15.4/18.2 | 15.1/17.4 | 16.3/21.6 | 18.6/21.9 | 20.6/23.1 |
| No. of atoms (Protein/ligands/water) | 5248/58/462 | 5196/54/476 | 5210/25/503 | 5192/54/222 | 10,161/50/17 | 14,387/195/41 |
| Model quality | ||||||
| RMSDs | ||||||
| Bond lengths (Å) | 0.009 | 0.009 | 0.008 | 0.012 | 0.002 | 0.003 |
| Bond angles (o) | 1.012 | 0.997 | 0.942 | 1.008 | 0.505 | 0.617 |
| Mean B-factor (Å2) | ||||||
| All atoms | 25.8 | 27.1 | 31.8 | 45.1 | 58.7 | 82.4 |
| Protein | 25.1 | 26.2 | 31.2 | 45.1 | 58.6 | 82.1 |
| Ligand | 27.6 | 32.1 | 20.9 | 44.8 | 41.6 | 106.6 |
| Water | 33.0 | 34.4 | 38.0 | 44.9 | 48.8 | 56.5 |
| Coordinate error (maximum likelihood) (Å) | 0.19 | 0.17 | 0.14 | 0.19 | 0.30 | 0.35 |
| Ramachandran plot | ||||||
| Most favored (%) | 97.6 | 97.6 | 97.1 | 97.9 | 96.1 | 95.6 |
| Additionally allowed (%) | 2.4 | 2.4 | 2.9 | 2.0 | 3.9 | 3.2 |
CaAcs2, Candida albicans Acs2.
a
Values in parenthesis are for the highest resolution shell.
b
Rmerge = ∑hkl∑i |Ii(hkl) - <I(hkl)>|/∑hkl∑iIi(hkl), where Ii(hkl) is the intensity measured for the ith reflection and <I(hkl)> is the average intensity of all reflections with indices hkl.
c
Rfactor = ∑hkl ||Fobs (hkl) | - |Fcalc (hkl) ||/∑hkl |Fobs (hkl)|; Rfree is calculated in an identical manner using 5% of randomly selected reflections that were not included in the refinement.