Table 2.
Data collection and structural refinement statistics.
| H257W-leukoPNP- DADMe-ImmG-PO4 (PDB ID 4EB8) |
H257W(f)-leukoPNP- DADMe-ImmG-PO4 (PDB ID 4EAR) |
H257W-leukoPNP- PO4 (PDB ID 4GKA) |
H257W-leukoPNP- guanine (PDB ID 4ECE) |
||
|---|---|---|---|---|---|
| Data collection statistics | |||||
| Space group | P212121 | P212121 | P21 | P21 | |
| Unit cell parameters | a (Å) | 55.75 | 55.92 | 53.88 | 77.55 |
| b (Å) | 131.04 | 131.10 | 233.67 | 129.68 | |
| c (Å) | 137.50 | 137.68 | 70.08 | 104.35 | |
| β (°) | - | - | 97.33 | 105.29 | |
| Temperature (K) | 100 | 100 | 100 | 100 | |
| Wavelength (Å) | 1.075 | 1.075 | 1.075 | 1.075 | |
| Resolution (Å) | 50–2.30 (2.38–2.30) | 50–1.70 (1.73–1.70) | 50–2.20 (2.28–2.20) | 50–2.60 (2.69–2.60) | |
| Rmerge (%) | 9.7 (82.8) | 5.8 (91.4) | 10.3 (87.6) | 7.0 (87.2) | |
| Completeness (%) | 99.9 (100) | 98.3 (97.4) | 100 (100) | 100 (100) | |
| I/σI | 20.8 (2.2) | 47.3 (2.6) | 19.4 (2.1) | 26.2 (2.0) | |
| Unique reflections | 45728 (4476) | 110270 (5375) | 86349 (8627) | 61417 (6104) | |
| Redundancy | 6.0 (5.9) | 8.0 (8.0) | 4.2 (4.2) | 4.2 (4.2) | |
| Mosaicity (°) | 0.9 | 0.4 | 0.5 | 0.3 | |
| B-factor from Wilson plot (A2) | 43 | 28 | 33 | 69 | |
| Refinement statistics | |||||
| Resolution (Å) | 47.48–2.30 | 41.24–1.70 | 45.29–2.20 | 49.04–2.60 | |
| Total number of reflections | 45558 | 110107 | 86296 | 61129 | |
| Working set: number of reflections | 43257 | 104515 | 81976 | 58023 | |
| Rfactor (%) | 18.11 | 17.47 | 18.80 | 22.15 | |
| Test set: number of reflections | 2301 | 5592 | 4320 | 3106 | |
| Rfree (%) | 22.76 | 20.29 | 23.20 | 26.10 | |
| Protein atoms | 6722 (A,B,C)1 | 6753 (A,B,C)1 | 12645 (A,B,C,D,E,F)1 | 13261 (A,B,C,D,E,F)1 | |
| Water atoms | 324 | 579 | 404 | 306 | |
| DADMe-ImmG atoms | 60 | 60 | - | - | |
| Phosphate atoms | 15 | 15 | 30 | - | |
| Guanine atoms | - | - | - | 66 | |
| Ethylene glycol atoms | 8 | - | - | - | |
| Glycerol atoms | 12 | ||||
| Geometry statistics | |||||
| Rmsd (bond distance) (Å) | 0.01 | 0.01 | 0.01 | 0.01 | |
| Rmsd (bond angle) (°) | 1.51 | 1.49 | 1.40 | 1.35 | |
| RmsdB | |||||
| Main chain bonded atoms (Å2) | 1.99 | 1.38 | 1.90 | 1.87 | |
| Side chain bonded atoms (Å2) | 2.74 | 2.25 | 2.48 | 2.26 | |
| Average B | |||||
| Main chain atoms (Å2) | 45.70 | 36.18 | 45.82 | 59.27(A,B,C)/85.49(D,E,F) | |
| Side chain atoms (Å2) | 49.76 | 41.36 | 50.38 | 62.45(A,B,C)/88.54(D,E,F) | |
| Water atoms (Å2) | 45.51 | 45.63 | 42.48 | 55.14 | |
| DAD-Me-ImmG atoms (Å2) | 32.68 | 26.06 | - | - | |
| Phosphate atoms (Å2) | 32.05 | 26.29 | 40.34 | - | |
| Guanine atoms (Å2) | - | - | - | 48.63 | |
| Ethylene glycol atoms (Å2) | 47.98 | - | - | - | |
| Glycerol atoms (Å2) | - | - | 47.83 | - | |
| Ramachandran plot | |||||
| Most favored region (%) | 93.1 | 93.5 | 93.5 | 93.3 | |
| Additionally allowed regions (%) | 6.3 | 5.9 | 6.1 | 5.9 | |
| Generously allowed regions (%) | 0.1 | 0.1 | 0 | 0.3 | |
| Disallowed regions (%)2 | 0.4 | 0.4 | 0.4 | 0.4 | |
1
ABC chains form one timer and DEF belong 10 another trimer
2
Thr221 of each monomer is close to allowed regions in the Ramachandran plot. In the crystal structures, Thr221 locates in one of the active site loops