Software | Name | Version | Classification |
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XSCALE | | data scalingPHASER | | phasingPHENIX | 1.8.4_1496refinementPDB_EXTRACT | 3.22 | data extractionXDS | | data reductionPHASER | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5KOB Resolution: 1.95→48.536 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.07
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1918 | 1926 | 3.26 % |
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Rwork | 0.1615 | - | - |
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obs | 0.1625 | 59092 | 99.76 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 123.7 Å2 / Biso mean: 47.11 Å2 / Biso min: 21.27 Å2 |
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Refinement step | Cycle: final / Resolution: 1.95→48.536 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4934 | 0 | 115 | 348 | 5397 |
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Biso mean | - | - | 66.48 | 48.96 | - |
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Num. residues | - | - | - | - | 640 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 5198 | X-RAY DIFFRACTION | f_angle_d1.062 | 7065 | X-RAY DIFFRACTION | f_chiral_restr0.047 | 777 | X-RAY DIFFRACTION | f_plane_restr0.006 | 938 | X-RAY DIFFRACTION | f_dihedral_angle_d13.498 | 1927 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.9499-1.9987 | 0.2624 | 132 | 0.2055 | 4034 | 4166 | 100 | 1.9987-2.0527 | 0.2503 | 135 | 0.1902 | 4045 | 4180 | 100 | 2.0527-2.1131 | 0.2105 | 142 | 0.1793 | 4008 | 4150 | 100 | 2.1131-2.1813 | 0.1968 | 125 | 0.1692 | 4048 | 4173 | 100 | 2.1813-2.2593 | 0.252 | 130 | 0.1799 | 4096 | 4226 | 100 | 2.2593-2.3497 | 0.24 | 134 | 0.173 | 4025 | 4159 | 100 | 2.3497-2.4567 | 0.2437 | 133 | 0.1821 | 4038 | 4171 | 100 | 2.4567-2.5862 | 0.2324 | 156 | 0.1778 | 4050 | 4206 | 100 | 2.5862-2.7482 | 0.2026 | 137 | 0.1824 | 4086 | 4223 | 100 | 2.7482-2.9604 | 0.2649 | 128 | 0.1775 | 4042 | 4170 | 100 | 2.9604-3.2582 | 0.193 | 153 | 0.1769 | 4096 | 4249 | 100 | 3.2582-3.7295 | 0.1721 | 135 | 0.1499 | 4136 | 4271 | 100 | 3.7295-4.6982 | 0.1464 | 145 | 0.1271 | 4152 | 4297 | 100 | 4.6982-48.5507 | 0.1687 | 141 | 0.1604 | 4310 | 4451 | 99 |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 2.4392 | 1.4432 | -1.9314 | 7.9607 | -1.8563 | 5.0045 | 0.0567 | -0.15 | 0.3018 | 0.4228 | -0.0728 | 0.6536 | -0.5174 | -0.537 | -0.0673 | 0.3032 | 0.0281 | 0.0177 | 0.2749 | -0.044 | 0.2835 | -22.0917 | 9.4963 | 1.2684 | 2 | 8.572 | 5.1989 | -6.6981 | 4.3882 | -5.8554 | 7.9824 | 0.1294 | -0.7364 | -0.1799 | 0.467 | -0.3827 | 0.2107 | 0.1755 | 0.3831 | 0.4031 | 0.406 | -0.0294 | 0.0583 | 0.3419 | -0.0108 | 0.2392 | -20.1314 | -4.5659 | 13.1852 | 3 | 5.3497 | -1.151 | 3.3502 | 8.549 | -5.8299 | 6.1907 | -0.2294 | -0.1593 | 0.5128 | 0.3053 | 0.3622 | 0.518 | -0.7757 | -2.2197 | -0.1856 | 0.2658 | 0.0436 | 0.0724 | 0.7153 | -0.0374 | 0.3754 | -32.5287 | 2.7362 | 11.0316 | 4 | 1.5779 | 0.2593 | -0.7161 | 7.5291 | 0.8177 | 3.3305 | -0.0603 | 0.0899 | -0.1294 | -0.4049 | -0.1733 | 0.6288 | 0.3801 | -0.7923 | 0.206 | 0.2802 | -0.0853 | 0.0174 | 0.3766 | -0.05 | 0.2412 | -28.8834 | -4.3661 | 3.0933 | 5 | 2.5685 | -0.5154 | 0.2352 | 6.0205 | -0.7416 | 3.4891 | 0.0643 | 0.1587 | -0.2057 | -0.2986 | -0.2112 | 0.1626 | 0.4653 | -0.3826 | 0.1607 | 0.2794 | -0.0681 | 0.0228 | 0.3264 | 0.0114 | 0.2151 | -26.7058 | -4.2159 | -12.1789 | 6 | 2.2726 | 0.8711 | -0.5352 | 3.2874 | 2.2303 | 3.6025 | 0.0945 | -0.2452 | -0.0289 | 0.7521 | -0.0587 | 0.3632 | 1.3853 | -0.3157 | 0.1886 | 0.5349 | -0.1415 | 0.0977 | 0.3419 | 0.0052 | 0.3331 | -28.5835 | -13.4934 | 6.1264 | 7 | 2.2124 | 0.2904 | -0.3731 | 2.9503 | -1.3204 | 5.2166 | -0.052 | -0.0127 | -0.2965 | 0.0159 | 0.0368 | 0.3133 | 0.6651 | -0.7811 | -0.0152 | 0.3633 | -0.0916 | 0.0588 | 0.2744 | -0.0044 | 0.242 | -28.161 | -9.3323 | -2.2941 | 8 | 4.6735 | -0.6804 | 4.018 | 4.7877 | -2.8933 | 4.7297 | 0.1838 | 0.3766 | -0.0915 | -0.0945 | 0.0234 | -0.1768 | 0.48 | 1.0574 | -0.1031 | 0.2335 | 0.0087 | -0.0101 | 0.2555 | -0.0017 | 0.2419 | -19.2363 | -0.1032 | -11.341 | 9 | 6.9213 | -0.4699 | -1.8609 | 2.3397 | 1.0853 | 4.8678 | 0.0312 | 0.1393 | 0.3512 | -0.3398 | 0.1176 | 0.3748 | -0.2852 | -0.5292 | -0.1745 | 0.2758 | 0.0087 | -0.038 | 0.3542 | 0.0339 | 0.3177 | -29.3355 | 6.8501 | -19.229 | 10 | 2.6154 | 2.9434 | -0.2119 | 8.7843 | -2.3068 | 3.9611 | 0.0348 | -0.2933 | -0.2323 | 0.7199 | -0.3053 | 0.0838 | 0.5761 | -0.5941 | 0.3219 | 0.3598 | -0.0509 | 0.0782 | 0.3244 | 0.0033 | 0.3077 | -26.3001 | -5.6537 | -34.2287 | 11 | 7.1864 | -1.7966 | 3.1648 | 7.4759 | -4.8023 | 3.5694 | -0.3662 | -0.6348 | -0.077 | 0.9776 | -0.2408 | -0.4851 | -0.4021 | 0.1489 | 0.8185 | 0.4281 | 0.0251 | 0.019 | 0.3626 | 0.0111 | 0.2189 | -12.9839 | -3.8457 | -21.7005 | 12 | 8.2937 | 0.888 | 3.4305 | 5.5902 | 0.7076 | 2.6568 | 0.2875 | -0.3084 | -0.7374 | -0.0404 | -0.2533 | 0.1888 | 1.6717 | -0.4824 | -0.0425 | 0.594 | -0.032 | 0.0399 | 0.2489 | 0.0599 | 0.3635 | -19.5405 | -16.1889 | -24.8436 | 13 | 6.5529 | -0.5474 | 1.2286 | 4.6667 | -0.8217 | 6.9716 | 0.0317 | 0.198 | -0.4414 | -0.16 | -0.0441 | 0.0919 | 0.8951 | -0.0334 | 0.0155 | 0.3038 | 0.0025 | 0.0489 | 0.2248 | 0.0389 | 0.209 | -17.691 | -10.6096 | -31.3394 | 14 | 2.6031 | 2.0532 | 1.2949 | 4.3766 | 4.1068 | 4.0218 | -1.3916 | 0.6818 | -1.711 | 0.105 | 1.105 | 0.3706 | -0.193 | -0.5236 | -0.0085 | 0.8481 | 0.1063 | 0.1503 | 0.6714 | -0.205 | 1.0368 | -9.7164 | -22.8488 | -37.5664 | 15 | 1.9399 | -1.1294 | -2.5671 | 0.8762 | 1.5018 | 7.3859 | 0.2127 | -0.3529 | 0.0599 | 0.4536 | -0.4682 | -0.4125 | 0.2268 | 1.2787 | 0.3032 | 0.2939 | 0.1488 | 0.0109 | 0.46 | 0.1257 | 0.3385 | -5.5385 | -8.4978 | -31.1777 | 16 | 2.1008 | 1.0242 | 3.5497 | 4.6287 | 0.7721 | 6.72 | -0.3452 | 0.8255 | -0.2609 | -0.5583 | 0.0507 | -0.5212 | 0.6472 | 1.5752 | 0.1137 | 0.3631 | 0.1823 | 0.0838 | 0.5969 | 0.1061 | 0.3107 | -5.451 | -8.8231 | -48.9884 | 17 | 2.3647 | -0.3492 | 1.1073 | 0.724 | -1.196 | 3.1155 | -0.0978 | -0.0468 | -0.3068 | 0.1164 | -0.0734 | -0.0606 | 0.6644 | 0.5379 | 0.1118 | 0.3874 | 0.1682 | 0.0347 | 0.3748 | 0.0375 | 0.2717 | -10.96 | -10.8163 | -37.8356 | 18 | 2.6677 | 0.0094 | 1.1283 | 1.3296 | 0.6192 | 4.8308 | -0.0413 | 0.0699 | -0.2442 | -0.0255 | -0.1012 | -0.1533 | 0.4301 | 0.7532 | 0.1326 | 0.2738 | 0.0874 | 0.0507 | 0.3328 | 0.0508 | 0.2334 | -10.2589 | -8.3083 | -40.2329 | 19 | 8.6357 | 0.591 | -0.1062 | 7.2777 | -0.5171 | 2.2613 | 0.1089 | 0.3604 | -0.7561 | -0.0804 | -0.0415 | 0.4567 | 0.8766 | -0.1197 | -0.027 | 0.403 | 0.0141 | -0.0381 | 0.325 | -0.0568 | 0.3115 | -22.7922 | -11.7483 | -55.0754 | 20 | 4.232 | 4.4146 | -0.2206 | 5.6941 | -1.4513 | 8.1468 | -0.0819 | 0.2198 | 0.6937 | -0.1412 | 0.3724 | 0.5905 | -0.4269 | -1.1734 | -0.2424 | 0.3108 | 0.0534 | -0.0542 | 0.3193 | 0.0753 | 0.3785 | -27.5035 | 14.4087 | -26.2892 | 21 | 4.8565 | 0.5337 | -1.5396 | 4.2425 | -5.5698 | 7.5144 | -0.238 | 1.1907 | 0.3627 | -1.8677 | 0.896 | 1.2077 | 0.1495 | -0.9042 | -0.3848 | 0.8634 | -0.1176 | -0.059 | 0.4594 | 0.0984 | 0.4192 | -18.8288 | 17.811 | -42.8941 | 22 | 5.9555 | -0.6707 | -1.161 | 6.2627 | 4.8211 | 4.5008 | 0.008 | 0.2078 | 0.9252 | 0.8736 | -0.0227 | 1.1585 | -2.5011 | -0.1471 | -0.0394 | 1.1288 | 0.0032 | 0.0737 | 0.2859 | 0.1235 | 0.6486 | -22.4836 | 28.2092 | -33.8738 | 23 | 2.8431 | 1.0505 | -2.779 | 6.6664 | -1.9967 | 5.7821 | 0.2713 | -0.1787 | 0.4065 | 0.3483 | 0.0501 | 0.1404 | -1.1551 | -0.062 | -0.2677 | 0.4527 | -0.0798 | -0.0208 | 0.3299 | 0.0362 | 0.3163 | -19.6147 | 20.9067 | -30.5822 | 24 | 6.6285 | 5.2111 | 6.6299 | 6.4533 | 4.4186 | 7.4679 | -0.2688 | -1.5868 | 1.6834 | 1.7739 | -1.173 | -0.7721 | -2.7873 | -0.6006 | 1.1313 | 0.9842 | -0.2049 | -0.075 | 0.654 | -0.0495 | 0.538 | -8.6356 | 30.1063 | -24.6209 | 25 | 4.2427 | 0.5364 | 1.1484 | 1.9198 | -1.0937 | 5.375 | -0.0312 | 0.5763 | 0.2273 | -0.5803 | -0.1269 | -0.0175 | -0.2543 | 0.5419 | 0.2365 | 0.4243 | -0.1539 | 0.0229 | 0.3873 | 0.0041 | 0.3308 | -8.4467 | 18.5639 | -35.3412 | 26 | 4.8918 | -3.2096 | -6.9413 | 4.5433 | 3.9161 | 2.1592 | -0.131 | -0.8801 | -0.0696 | 0.0785 | 0.2516 | -0.753 | 0.4807 | 1.2376 | -0.1928 | 0.309 | 0.038 | -0.0008 | 0.7231 | 0.0948 | 0.5423 | -2.9051 | 13.1043 | -19.0704 | 27 | 3.5879 | 1.1514 | -1.8745 | 1.9117 | -2.0936 | 4.5044 | -0.132 | 0.1877 | 0.1974 | -0.2252 | 0.1017 | -0.1765 | -0.4179 | 0.4092 | 0.0432 | 0.3878 | -0.1452 | -0.003 | 0.313 | 0.0042 | 0.3251 | -11.2126 | 18.6162 | -26.8937 | 28 | 3.7096 | 0.4702 | -1.2062 | 3.3558 | -1.2879 | 3.5834 | -0.2538 | 0.1494 | 0.1828 | -0.2433 | 0.2547 | -0.3992 | -0.5971 | 0.7546 | -0.025 | 0.3703 | -0.1618 | 0.0152 | 0.4087 | 0.0158 | 0.2937 | -8.0092 | 19.139 | -28.5251 | 29 | 3.6372 | 2.4813 | -1.1035 | 6.7473 | 2.9508 | 3.0984 | -0.381 | -0.4632 | -0.4327 | 0.1485 | 0.1964 | -0.133 | 0.2752 | 1.1338 | 0.0762 | 0.2226 | 0.0327 | -0.0002 | 0.4015 | 0.0816 | 0.3133 | -14.4694 | 8.0443 | -20.0657 | 30 | 2.2797 | 0.0051 | 0.2987 | 9.2599 | 0.1046 | 3.0009 | -0.3268 | -0.5219 | 0.3105 | 0.7256 | -0.1977 | 0.0266 | -1.1074 | 1.2083 | 0.5304 | 0.4415 | -0.0754 | 0.0056 | 0.4218 | 0.068 | 0.4007 | -16.9663 | 14.5599 | -7.2256 | 31 | 7.5533 | -0.3543 | 4.9639 | 3.7954 | -0.4202 | 6.3739 | 0.202 | -0.2855 | -0.522 | -0.3576 | -0.2014 | 0.5162 | 1.0545 | -0.7539 | -0.0879 | 0.3883 | -0.0754 | -0.0675 | 0.3292 | -0.0731 | 0.402 | -30.6294 | -9.4577 | -62.7091 | 32 | 3.5713 | -0.938 | 4.2614 | 1.3956 | -1.7683 | 5.6289 | 0.8161 | 1.3377 | -0.4268 | -1.0218 | -0.5487 | 0.5089 | 0.7641 | 0.2921 | -0.3508 | 0.6509 | 0.2269 | -0.1836 | 0.7379 | -0.0885 | 0.445 | -32.145 | -0.6378 | -78.8731 | 33 | 6.0708 | -0.4477 | -0.7082 | 6.5697 | -2.925 | 8.4139 | -0.0122 | 0.0448 | -0.5341 | -0.7297 | -0.2959 | 1.7185 | 0.3984 | -2.1537 | -0.2906 | 0.3808 | 0.0151 | -0.2376 | 0.9572 | -0.2164 | 0.9328 | -43.4005 | -4.1221 | -70.5444 | 34 | 3.9367 | 0.2025 | 0.1094 | 6.266 | -2.2701 | 4.2648 | 0.1361 | 0.2147 | 0.2386 | -0.0288 | -0.1019 | 0.7222 | -0.3429 | -0.7604 | -0.0352 | 0.2924 | 0.12 | -0.0738 | 0.4338 | -0.1032 | 0.3982 | -36.3987 | 3.7203 | -67.452 | 35 | 3.2463 | -1.2048 | 0.2515 | 8.3663 | -3.2267 | 8.9229 | -0.1214 | -0.0949 | 0.4257 | 0.4947 | -0.3738 | -0.1737 | -1.1663 | -0.3673 | 0.3789 | 0.3037 | 0.0646 | -0.0948 | 0.3247 | -0.0448 | 0.3193 | -29.2524 | 8.3492 | -54.2007 | 36 | 4.5186 | 2.0904 | 2.6168 | 8.8535 | 3.3405 | 6.9795 | -0.3922 | 0.4336 | 0.4894 | -0.8408 | 0.0598 | 0.9049 | -1.1229 | -0.517 | 0.5161 | 0.601 | 0.2434 | -0.1466 | 0.576 | 0.0189 | 0.521 | -36.2729 | 12.0432 | -72.7341 | 37 | 1.8513 | -0.0277 | 0.1653 | 3.7056 | -1.4522 | 4.337 | -0.126 | -0.0454 | 0.2621 | 0.0584 | 0.0128 | 0.2978 | -0.8464 | -0.6597 | 0.0805 | 0.3276 | 0.1154 | -0.0588 | 0.3195 | -0.0329 | 0.3093 | -30.4034 | 7.8658 | -61.5788 | 38 | 8.7531 | -0.0659 | -1.0179 | 9.3338 | -0.355 | 7.6314 | -0.1813 | -0.3192 | 0.192 | 0.6958 | 0.1655 | 0.6208 | -0.4503 | -0.8221 | -0.0109 | 0.3486 | 0.0669 | 0.0183 | 0.421 | -0.0172 | 0.2966 | -30.3316 | 0.1937 | -43.3081 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 2 through 14 )A2 - 14 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 15 through 25 )A15 - 25 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 26 through 41 )A26 - 41 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 42 through 87 )A42 - 87 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 88 through 112 )A88 - 112 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 113 through 125 )A113 - 125 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 126 through 147 )A126 - 147 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 148 through 157 )A148 - 157 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 158 through 169 )A158 - 169 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 2 through 14 )B2 - 14 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 15 through 25 )B15 - 25 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 26 through 41 )B26 - 41 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 42 through 61 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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