Table 1.
Data collection and refinement statistics
NUDT15 | WT | V18I | R139C | R139H | V18_V19insGV |
---|---|---|---|---|---|
Data collection | |||||
Synchrotron and beamline | MAXIV BioMAX | MAXIV BioMAX | MAXIV BioMAX | MAXIV BioMAX | DLS I24 |
Space group | P 1 21 1 | C 1 2 1 | P 1 | P 1 | P 1 21 1 |
Cell dimensions | |||||
a,b,c (Å) | 63.6, 45.6, 67.0 | 115.5, 34.6, 75,2 | 34.9, 43.8, 60.4 | 41.3, 60.2, 69.3 | 63.4, 45.7, 66.3 |
α, β, γ (°) | 90, 116, 90 | 90.0, 148.6, 90.0 | 91.6, 106.7, 113.48 | 100.1, 104.1, 90.3 | 90, 115.1, 90 |
Resolution (Å) | 60.24–1.60 (1.63–1.60)a | 39.22–1.50 (1.53–1.50)a | 35.37–1.60 (1.63–1.60)a | 40.59–1.60 (1.63–1.60)a | 60.07–1.45 (1.47–1.45) |
Rmeas | 0.064 (0.721)a | 0.119 (0.886)a | 0.059 (0.148)a | 0.060 (0.305)a | 0.086 (1.458)a |
Rpim | 0.034 (0.385)a | 0.062 (0.472)a | 0.042 (0.105)a | 0.042 (0.216)a | 0.021 (0.362)1 |
CC1/2 | 0.999 (0.862)a | 0.994 (0.949)a | 0.997 (0.985)a | 0.998 (0.976)a | 1.000 (0.861)a |
<I/σ(I)> | 15.1 (2.4)a | 8.6 (1.8)a | 16.2 (7.6)a | 11.5 (2.7)a | 24.7 (3.1)a |
Total observations | 310,958 (15,401)a | 166,790 (8167)a | 140,950 (6.909)a | 289,021 (14,047)a | 1,931,455 (93,528)a |
Unique observations | 45,919 (2312)a | 25,129 (1235)a | 39,574 (1931)a | 81,339 (3976)a | 61,265 (3026)a |
Completeness (%) | 100 (100)a | 100 (100)a | 96.6 (95.2)a | 96.8 (95.3)a | 100 (100)a |
Redundancy | 6.8 (6.7)a | 6.6 (6.6)a | 3.6 (3.6)a | 3.6 (3.5)a | 31.5 (30.9)a |
Refinement | |||||
Rwork/Rfree | 0.167/0.196 | 0.180/0.213 | 0.160/0.184 | 0.185/0.220 | 0.167/0.197 |
B-factors (A2): | |||||
Protein | 25.5 | 42.3 | 23.1 | 33.1 | 21.4 |
Solvent | 37.6 | 51.8 | 34.8 | 27.2 | 35.6 |
Ligand | 20.2 | 39.8 | 24.0 | 39.0 | 17.5 |
R.m.s.d. bond lengths (Å) | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 |
R.m.s.d. bond angles (°) | 1.82 | 1.74 | 1.89 | 1.70 | 1.86 |
Ramachandran statistics: | |||||
Favored (%) | 98.1 | 96.7 | 98.7 | 97.6 | 98.71 |
Outliers (%) | 0 | 0 | 0 | 0 | 0.32 |
PDB ID | 7B63 | 7B64 | 7B65 | 7B66 | 7B67 |
Values in parentheses are for the highest-resolution shell.