Table 1 Data collection and refinement statistics of PcUP crystals.
From: Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici
PcUP1 SeMet | PcUP1 | PcUP1 URA/R1P | PcUP1 DUR/PO4 | PcUP1 THM/PO4 | |
|---|---|---|---|---|---|
Data collectin | |||||
Space group | P222 | P21 | p212121 | p212121 | P222 |
Cell dimensions | |||||
a, b, c (Å) | 51.38, 87.72, 119.472 | 67.24, 153.05, 67.28 | 66.975, 97.68, 188.865 | 66.790, 97.38, 188.520 | 66.956, 97.33, 188.346 |
β(°) | 90.000 | 115.74 | 90.000 | 90.000 | 90.000 |
Resolution (Å) | 50–2.17 (2.21–2.1) | 50–1.57 (1.63–1.57) | 50–2.5 (2.54–2.5) | 50–2.10 (2.14–2.10) | 50–1.97 (2.00–1.7) |
Rmerge (%) | 22.9 (151.8) | 15.9 (81.4) | 15.3(55.9) | 16.6(49.6) | 19.9(98.4) |
I/σ | 13.54(1) | 6.6(1) | 20.7 (5.7) | 16.9(6.7) | 11.9(2.1) |
Completeness (%) | 99.9(100) | 98.9(83.1) | 100 (100) | 99.9 (100) | 99.7 (93.8) |
Redundancy | 13.3 (10.8) | 3.4 (3.0) | 13.3 (13.2) | 13.9(13.3) | 12.5(11.1) |
Refinement | |||||
Resolution (Å) | 19.57–2.0 (2.2–2.0) | 47.51–1.57 (1.63–1.57) | 48.84–2.50 (2.59–2.50) | 48.69–2.10 (2.17–2.10) | 38.46–1.96 (2.03–16) |
No. reflections | 32841 | 144078 (5837) | 43174 (4118) | 72543 (7120) | 87357(8200) |
Rwork/Rfree | 31.06 (24.18)/30 (23) | 18.6(19.1)/21.7 (22) | 26.1 (25.6)/34.8 (34.9) | 24.62 (25.57)/31.7 (31.58) | 26.5 (29.2)/31.56(32.85) |
No. atoms | |||||
Protein | 4298 | 8814 | 8580 | 8606 | 8595 |
Ligand/ion | 0 | 36 | 88 | 84 | 90 |
Water | 197 | 1280 | 190 | 533 | 584 |
B-factors | |||||
Protein | 19.3 | 17.3 | 39.7 | 30.2 | 29.7 |
Ligand/ion | - | 13.7 | 31.9 | 23.9 | 27.3 |
Water | 27.7 | 28.7 | 35.1 | 32.2 | 34.2 |
R.m.s. deviations | |||||
Bond lengths (Å) | 0.01 | 0.0062 | 0.01 | 0.0091 | 0.010 |
Bond angles (°) | 1.17 | 0.84 | 1.15 | 1.06 | 1.20 |
Ramachandran plot [%] | |||||
Most favored | 95.79 | 96.7 | 94.0 | 94.5 | 95.43 |
Additionally allowed | 4.21 | 3.07 | 5.45 | 4.64 | 3.87 |
