Table 1 Data collection and refinement statistics.
Dop-PupQ-AMP-PCP | Dop-PupE-ADP-MgF3(H2O)‾ | Dop-PupEP-ADP | Dop-PupE-ADP-MgF42− | Dop (Dop-loop-inserted) | |
|---|---|---|---|---|---|
PDB ID | 7OXY | 7OYF | 7OY3 | 7OYH | 7OXV |
Crystal form | |||||
Space group | P 31 2 1 | P 31 2 1 | P 31 2 1 | P 31 2 1 | P 41212 |
Unit cell | 106.668 | 106.334 | 106.806 | 106.827 | 72.533 |
dimensions (Å) | 106.668 | 106.334 | 106.806 | 106.827 | 72.533 |
108.791 | 107.384 | 108.457 | 107.947 | 184.149 | |
angels α, β, γ (°) | 90 90 120 | 90 90 120 | 90 90 120 | 90 90 120 | 90 90 90 |
Molecules/ASU | 1 | 1 | 1 | 1 | 1 |
Data collection | |||||
Wavelength (Å) | 1.000 | 1.000 | 0.815 | 1.000 | 1.000 |
Resolution (Å) | 46.19–1.65 | 47.65–1.88 | 46.78–1.78 | 47.87–1.75 | 46.04–1.39 |
(1.709–1.65) | (1.947–1.88) | (1.844–1.78) | (1.813–1.75) | (1.444–1.39) | |
Total reflections | 1,743,812 (177,795) | 1,162,055 (111,367) | 1,419,633 (139,117) | 1,445,395 (146,848) | 2,479,743 (216,822) |
Unique reflections | 86,165 (8,506) | 57,433 (5,667) | 68,753 (6,798) | 72,028 (7,143) | 98,553 (9,612) |
Multiplicity | 20.2 (20.9) | 20.2 (19.7) | 20.6 (20.5) | 20.1 (20.6) | 25.2 (22.6) |
Completeness (%) | 99.98 (99.99) | 99.98 (99.98) | 99.92 (99.96) | 99.94 (99.89) | 99.85 (98.99) |
Mean I/σ(I) | 21.30 (1.80) | 17.14 (2.03) | 12.56 (1.38) | 17.52 (2.33) | 26.76 (1.24) |
Wilson B-factor (Å2) | 27.75 | 29.56 | 24.81 | 23.38 | 19.73 |
Rmerge | 0.084 (1.858) | 0.124 (1.625) | 0.168 (1.178) | 0.150 (1.934) | 0.069 (2.239) |
Rmeas | 0.086 (1.905) | 0.128 (1.668) | 0.172 (1.208) | 0.154 (1.983) | 0.070 (2.290) |
CC1/2 | 1 (0.746) | 0.999 (0.804) | 0.999 (0.774) | 0.999 (0.798) | 1 (0.587) |
Refinement | |||||
Reflections used | 86,152 (8,505) | 57,429 (5,666) | 68,738 (6,797) | 71,997 (7,135) | 98,538 (9,599) |
Reflections used Rfree | 4,381 (410) | 2,960 (279) | 3,271 (300) | 3,621 (346) | 4,965 (475) |
Rwork | 0.1729 (0.2629) | 0.1592 (0.2178) | 0.1701 (0.2808) | 0.1619 (0.2391) | 0.1334 (0.2561) |
Rfree | 0.1951 (0.2774) | 0.1878 (0.2676) | 0.1955 (0.2880) | 0.1842 (0.2696) | 0.1691 (0.3181) |
Model composition | |||||
Non-hydrogen atoms | 4,490 | 4,462 | 4,595 | 4,638 | 4,805 |
Macromolecules | 4,045 | 4,050 | 4,031 | 4,087 | 4,283 |
Ligands | 119 | 111 | 101 | 177 | 68 |
Water | 326 | 301 | 463 | 374 | 454 |
Protein residues | 501 | 501 | 499 | 499 | 501 |
RMSD | |||||
Bonds | 0.007 | 0.010 | 0.007 | 0.007 | 0.009 |
Angles | 0.89 | 1.10 | 0.90 | 0.92 | 1.09 |
Ramachandran plot | |||||
Favored (%) | 98.38 | 98.58 | 98.37 | 98.37 | 98.39 |
Allowed (%) | 1.62 | 1.42 | 1.63 | 1.63 | 1.61 |
Outliers (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
Rotamer outliers (%) | 0.23 | 0.23 | 0.23 | 0.00 | 0.86 |
Clashscore | 3.87 | 3.63 | 6.61 | 4.13 | 4.10 |
Average B-factor | 33.43 | 33.94 | 30.59 | 28.46 | 28.33 |
Macromolecules | 32.44 | 33.00 | 29.37 | 26.99 | 26.49 |
Ligands | 47.52 | 50.35 | 41.78 | 43.81 | 67.64 |
Water | 40.57 | 40.50 | 38.74 | 37.29 | 39.71 |
