Table 1 Data collection and refinement statistics
From: Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI
McyI with | prebound NAD | soaked NAD | soaked NADP | R166M with citrate | R166A with citrate | R166M with malate | R166A with malate |
|---|---|---|---|---|---|---|---|
PDB code | 8WPH | 8WPJ | 8WPI | 8WPQ | 8WPO | 8WPS | 8WPR |
Data collection | |||||||
Space group | P41 | P41 | P41 | p3121 | p3121 | p3121 | p3121 |
Wavelength | 0.9792 | 0.9792 | 0.9792 | 0.9792 | 0.9792 | 0.9792 | 0.9792 |
Resolution (Å) | 50.00–2.80 (2.90–2.80) | 50.00–2.80 (2.90–2.80) | 50.00–2.20 (2.28–2.20) | 50.00–2.60 (2.69–2.60) | 50.00–2.10 (2.18–2.10) | 50.00–1.90 (1.97–1.90) | 50.00–1.70 (1.76–1.70) |
Unit cell | |||||||
a, b, c (Ã…) | 74.0, 74.0, 128.5 | 75.1, 75.1, 127.3 | 74.5, 74.5, 127.8 | 61.2, 61.2, 173.9 | 61.5, 61.5, 173.0 | 61.1, 61.1, 173.1 | 61.2, 61.2, 173.6 |
α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 |
Total reflections | 640499 | 696550 | 1021315 | 576675 | 1488500 | 865746 | 1406507 |
Unique reflections | 17029 (1700) | 17359 (1736) | 35329 (3499) | 12233(1206) | 23011(2243) | 56839(5705) | 42382(4017) |
Redundancy | 6.5 (6.9) | 5.4 (5.5) | 13.6 (14.0) | 5.3 (5.3) | 19.1(19.8) | 5.9 (5.9) | 18.0(13.5) |
Completeness (%) | 99.6 (100) | 99.6 (100) | 100 (99.9) | 99.5 (99.8) | 99.6 (99.2) | 100 (100) | 99.7(97.6) |
I/σI | 16.9 (2.1) | 14.3 (2.0) | 27.5 (2.7) | 15.3 (1.7) | 35.2(2.0) | 16.0 (1.6) | 44.7(3.0) |
Rmergea | 0.129 (1.008) | 0.163 (1.182) | 0.108 (1.105) | 0.097(0.862) | 0.092 (1.613) | 0.122(1.341) | 0.119 (0.992) |
Rpimb | 0.050 (0.384) | 0.069 (0.500) | 0.029 (0.291) | 0.041(0.355) | 0.021 (0.356) | 0.050 (0.548) | 0.029 (0.263) |
CC1/2 | 0.992 (0.776) | 0.984 (0.675) | 0.996 (0.809) | 0.991(0.683) | 0.996 (0.731) | 0.993(0.494) | 0.997 (0.818) |
Refinement | |||||||
Resolution (Å) | 48.48–2.80 (2.90–2.80) | 48.98–2.80 (2.90–2.80) | 37.27–2.20 (2.28–2.20) | 29.07–2.60 (2.69–2.60) | 39.13–2.10 (2.18–2.10) | 30.54–1.90 (1.97–1.90) | 45.22–1.70 (1.76–1.70) |
Rworkb/Rfreec | 0.195/0.246 | 0.200/0.254 | 0.176/0.207 | 0.214/0.263 | 0.226/0.256 | 0.171/0.207 | 0.167/0.178 |
No. of molecules | 2 | 2 | 2 | 1 | 1 | 1 | 1 |
No. of atoms | 4976 | 5042 | 5313 | 2565 | 2816 | 2778 | 2891 |
Protein | 4793 | 4860 | 4860 | 2427 | 2424 | 2471 | 2496 |
Ligand | 88 | 176 | 236 | 57 | 105 | 53 | 59 |
Water | 95 | 6 | 217 | 81 | 287 | 254 | 336 |
Average B (Ã…2) | 56.80 | 86.48 | 63.49 | 36.08 | 31.00 | 38.19 | 30.02 |
Protein | 57.67 | 86.66 | 63.82 | 36.26 | 30.19 | 37.78 | 28.96 |
Ligand | 33.07 | 82.01 | 62.99 | 32.75 | 39.01 | 33.75 | 26.14 |
Water | 34.66 | 67.74 | 56.81 | 33.13 | 34.91 | 43.12 | 38.57 |
R.m.s deviations | |||||||
Bond lengths (Ã…) | 0.005 | 0.003 | 0.004 | 0.003 | 0.004 | 0.007 | 0.006 |
Bond angles (°) | 0.83 | 0.59 | 0.68 | 0.59 | 0.768 | 0.993 | 1.005 |
Ramachandran plot | |||||||
Favored (%) | 94.46 | 96.52 | 96.68 | 96.20 | 96.20 | 96.86 | 96.86 |
Allowed (%) | 5.54 | 3.48 | 3.32 | 3.80 | 3.80 | 3.14 | 3.14 |
