Software | Name | Version | Classification |
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Blu-Ice | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.7_650)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TFD Resolution: 1.991→43.591 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 16.26 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1731 | 4045 | 5.08 % |
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Rwork | 0.1558 | - | - |
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obs | 0.1567 | 79661 | 95.96 % |
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all | - | 79661 | - |
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.228 Å2 / ksol: 0.448 e/Å3 |
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Refinement step | Cycle: LAST / Resolution: 1.991→43.591 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2886 | 0 | 111 | 170 | 3167 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 3139 | X-RAY DIFFRACTION | f_angle_d1.227 | 4287 | X-RAY DIFFRACTION | f_dihedral_angle_d15.239 | 1132 | X-RAY DIFFRACTION | f_chiral_restr0.064 | 434 | X-RAY DIFFRACTION | f_plane_restr0.004 | 554 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.991-2.0144 | 0.2577 | 145 | 0.2528 | 2412 | X-RAY DIFFRACTION | 87 | 2.0144-2.0389 | 0.2795 | 143 | 0.2312 | 2351 | X-RAY DIFFRACTION | 88 | 2.0389-2.0648 | 0.2592 | 130 | 0.2203 | 2467 | X-RAY DIFFRACTION | 90 | 2.0648-2.0919 | 0.2072 | 135 | 0.2084 | 2462 | X-RAY DIFFRACTION | 92 | 2.0919-2.1206 | 0.2295 | 131 | 0.2 | 2446 | X-RAY DIFFRACTION | 91 | 2.1206-2.1509 | 0.2228 | 135 | 0.202 | 2521 | X-RAY DIFFRACTION | 93 | 2.1509-2.183 | 0.1841 | 120 | 0.1872 | 2468 | X-RAY DIFFRACTION | 92 | 2.183-2.2171 | 0.1846 | 127 | 0.1842 | 2579 | X-RAY DIFFRACTION | 93 | 2.2171-2.2534 | 0.2111 | 155 | 0.1666 | 2570 | X-RAY DIFFRACTION | 95 | 2.2534-2.2923 | 0.1639 | 130 | 0.1602 | 2568 | X-RAY DIFFRACTION | 95 | 2.2923-2.334 | 0.1625 | 166 | 0.1614 | 2543 | X-RAY DIFFRACTION | 96 | 2.334-2.3789 | 0.2126 | 118 | 0.1531 | 2648 | X-RAY DIFFRACTION | 95 | 2.3789-2.4274 | 0.1705 | 134 | 0.1698 | 2619 | X-RAY DIFFRACTION | 96 | 2.4274-2.4802 | 0.1596 | 152 | 0.1665 | 2630 | X-RAY DIFFRACTION | 97 | 2.4802-2.5379 | 0.206 | 132 | 0.1609 | 2620 | X-RAY DIFFRACTION | 98 | 2.5379-2.6013 | 0.1582 | 131 | 0.1638 | 2655 | X-RAY DIFFRACTION | 98 | 2.6013-2.6717 | 0.1753 | 123 | 0.1713 | 2698 | X-RAY DIFFRACTION | 99 | 2.6717-2.7503 | 0.1829 | 157 | 0.1695 | 2623 | X-RAY DIFFRACTION | 98 | 2.7503-2.839 | 0.2083 | 153 | 0.1697 | 2642 | X-RAY DIFFRACTION | 98 | 2.839-2.9405 | 0.2039 | 166 | 0.1732 | 2677 | X-RAY DIFFRACTION | 99 | 2.9405-3.0582 | 0.1661 | 124 | 0.1581 | 2724 | X-RAY DIFFRACTION | 100 | 3.0582-3.1973 | 0.1603 | 161 | 0.1539 | 2667 | X-RAY DIFFRACTION | 99 | 3.1973-3.3658 | 0.2085 | 140 | 0.1516 | 2716 | X-RAY DIFFRACTION | 100 | 3.3658-3.5766 | 0.1543 | 110 | 0.1495 | 2745 | X-RAY DIFFRACTION | 100 | 3.5766-3.8526 | 0.1453 | 149 | 0.1394 | 2722 | X-RAY DIFFRACTION | 100 | 3.8526-4.24 | 0.1217 | 138 | 0.1174 | 2713 | X-RAY DIFFRACTION | 100 | 4.24-4.8529 | 0.1249 | 124 | 0.1163 | 2723 | X-RAY DIFFRACTION | 100 | 4.8529-6.1114 | 0.1718 | 168 | 0.1445 | 2688 | X-RAY DIFFRACTION | 100 | 6.1114-43.6018 | 0.1899 | 148 | 0.1791 | 2719 | X-RAY DIFFRACTION | 100 |
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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 | 2.2463 | 0.1658 | 0.4113 | 1.3562 | -0.5407 | 0.318 | -0.0762 | -0.5515 | -0.2824 | 0.3094 | 0.1087 | -0.1745 | 0.0671 | 0.315 | -0.0141 | 0.3057 | 0.0571 | -0.0204 | 0.4808 | 0.0069 | 0.2695 | 49.3508 | 46.7867 | 74.0753 | 2 | 0.6304 | -0.1464 | -0.133 | 0.6436 | -0.2015 | 0.1287 | -0.3956 | -0.7054 | -0.0717 | 0.6586 | 0.1705 | -0.006 | 0.124 | 0.0684 | 0.0178 | 0.5099 | 0.1825 | 0.0242 | 0.712 | 0.1752 | 0.3483 | 50.7643 | 40.2376 | 83.2729 | 3 | 0.4308 | 0.3917 | 0.6091 | 0.8834 | 0.4858 | 0.8714 | -0.4384 | -0.399 | -0.9285 | -0.0968 | 0.035 | 0.1186 | 0.3327 | 0.3255 | 0.0692 | 0.3051 | 0.1203 | 0.0948 | 0.4437 | 0.172 | 0.4313 | 49.727 | 35.9904 | 70.7167 | 4 | 0.6761 | -0.8862 | -0.4936 | 1.3846 | 0.2928 | 0.9199 | -0.3573 | -0.7278 | -0.4994 | 0.4183 | 0.3 | 0.5432 | 0.1042 | -0.0104 | 0.0001 | 0.4044 | 0.122 | 0.112 | 0.6165 | 0.1898 | 0.4188 | 40.1859 | 42.5777 | 79.8991 | 5 | 2.9376 | 0.8281 | -0.1235 | 1.9111 | -0.7617 | 0.3694 | -0.0969 | -0.5955 | -0.1777 | 0.4406 | -0.0252 | -0.0532 | -0.3738 | 0.3788 | 0.0401 | 0.2994 | 0.0129 | 0.0152 | 0.3971 | -0.0072 | 0.2313 | 44.7084 | 53.5158 | 73.813 | 6 | 1.521 | 0.529 | -0.4174 | 0.7734 | 0.0462 | 1.4518 | -0.1858 | -0.6596 | -0.019 | 0.0042 | 0.0282 | -0.1388 | -0.1368 | 0.1422 | 0.0434 | 0.2771 | -0.0055 | 0.0195 | 0.4083 | 0.0404 | 0.2988 | 49.3444 | 59.1761 | 59.99 | 7 | 0.06 | 0.1038 | -0.0245 | 1.021 | -0.1627 | 0.2757 | 0.0992 | 0.0973 | 0.0162 | -0.2119 | -0.3831 | -0.1928 | 0.0698 | -0.1433 | 0.1656 | 0.3627 | 0.0132 | 0.0269 | 0.3357 | 0.0163 | 0.2486 | 40.644 | 56.9111 | 57.1329 | 8 | 1.7645 | -2.1975 | -0.2158 | 3.5636 | 0.5191 | 1.2183 | 0.3716 | 0.3391 | -0.2633 | -0.6707 | -0.4255 | 0.2262 | -0.1489 | -0.1817 | 0.0307 | 0.3442 | 0.0235 | -0.0261 | 0.358 | -0.0396 | 0.296 | 34.6811 | 53.7501 | 59.7413 | 9 | 0.7885 | -0.3517 | -0.355 | 0.2818 | 0.5295 | 1.2611 | 0.0605 | 0.139 | -0.1518 | -0.1784 | -0.2161 | 0.1424 | -0.1662 | -0.2059 | 0.0641 | 0.3238 | -0.0035 | -0.009 | 0.3442 | -0.029 | 0.2617 | 30.619 | 56.2252 | 65.402 | 10 | 0.2811 | -0.0959 | -0.0646 | 0.4582 | 0.1949 | 0.3107 | 0.0161 | -0.1648 | -0.0249 | 0.2325 | -0.0445 | -0.0396 | -0.1138 | 0.0399 | -0.0077 | 0.3338 | -0.0064 | 0.0308 | 0.3427 | -0.0566 | 0.2709 | 37.4553 | 62.2496 | 71.2709 | 11 | 0.5272 | -0.5066 | 0.0773 | 0.5623 | 0.1287 | 1.2272 | 0.044 | 0.2058 | -0.1445 | -0.1163 | -0.1078 | 0.2096 | -0.1651 | -0.1615 | 0.0324 | 0.3181 | -0.01 | 0.0293 | 0.3205 | -0.0609 | 0.2875 | 27.642 | 58.9619 | 68.9842 | 12 | 0.9949 | 0.222 | -0.9871 | 1.3019 | -0.7643 | 1.7254 | 0.1625 | -0.0339 | 0.1878 | -0.3326 | -0.1422 | 0.3127 | -0.3029 | 0.0032 | -0.058 | 0.4013 | 0.0352 | -0.0002 | 0.2678 | -0.0096 | 0.2772 | 17.8474 | 80.8273 | 78.6148 | 13 | 0.2288 | 0.0144 | -0.1142 | 0.0304 | -0.0051 | 0.6709 | 0.1858 | 0.4002 | 0.0355 | -0.3556 | -0.3459 | 0.3242 | -0.7785 | -0.1527 | 0.2791 | 0.672 | 0.208 | -0.1728 | 0.4572 | -0.0386 | 0.354 | 11.3351 | 81.7685 | 69.2163 | 14 | 1.0103 | 0.4781 | -0.2053 | 0.4606 | -0.4632 | 0.6153 | 0.0613 | -0.0743 | -0.138 | -0.1878 | -0.3831 | 0.6369 | -0.3182 | -0.4309 | -0.0806 | 0.3744 | 0.1466 | -0.11 | 0.3522 | -0.1219 | 0.4101 | 6.9842 | 81.1204 | 81.696 | 15 | 1.6701 | -0.877 | 0.1302 | 1.3775 | 1.2362 | 1.8656 | 0.2112 | 0.4912 | -0.3271 | -0.3498 | -0.3259 | 0.3646 | -0.3699 | -0.2499 | 0.048 | 0.4145 | 0.0669 | -0.1063 | 0.3947 | -0.0831 | 0.3602 | 13.8703 | 71.3877 | 72.9776 | 16 | 1.1462 | 0.2933 | 1.1278 | 0.6494 | 0.6674 | 1.3573 | -0.2361 | 0.1754 | 0.1011 | -0.2316 | 0.0188 | 0.1125 | -0.3943 | 0.2424 | 0.1052 | 0.3502 | -0.0129 | -0.0256 | 0.2618 | -0.025 | 0.2453 | 25.639 | 78.4138 | 83.3895 | 17 | 1.4509 | 1.0653 | -0.3711 | 2.0397 | -1.0152 | 0.5527 | 0.2147 | 0.7579 | -0.0003 | -0.3176 | 0.1989 | 0.0458 | 0.389 | 0.2306 | -0.161 | 0.3667 | 0.0487 | -0.0412 | 0.444 | -0.0472 | 0.2663 | 35.512 | 72.1403 | 93.5972 | 18 | 0.7995 | 0.4398 | -1.0064 | 2.4483 | -0.3731 | 1.2832 | -0.3148 | -0.5017 | 0.3198 | 0.4744 | -0.0752 | -0.2576 | -0.1989 | -0.5425 | -0.1256 | 0.345 | 0.0378 | -0.0572 | 0.39 | -0.0913 | 0.222 | 23.0534 | 74.3922 | 97.6838 | 19 | 2.9094 | -1.9521 | -0.3615 | 1.7241 | -0.18 | 0.9276 | -0.1675 | -0.5472 | -0.1015 | 0.3149 | 0.2203 | 0.153 | 0.1496 | 0.1421 | -0.0084 | 0.3415 | 0.0271 | 0.0023 | 0.3088 | -0.0208 | 0.3035 | 24.8519 | 66.7868 | 93.5052 | 20 | 0.4542 | -0.1032 | -0.6995 | 0.8184 | -0.0082 | 1.1094 | -0.0048 | -0.122 | -0.0386 | -0.0459 | -0.0474 | 0.0137 | 0.1255 | 0.2273 | 0.0214 | 0.3165 | -0.0023 | 0.0153 | 0.3212 | -0.0244 | 0.2444 | 31.5059 | 66.7172 | 84.2105 | 21 | 3.4259 | -0.4935 | 0.1479 | 0.6065 | -0.0026 | 2.0963 | -0.2141 | 0.2306 | -0.2094 | -0.1665 | 0.2262 | 0.0035 | 0.6184 | 0.0622 | -0.0178 | 0.3752 | -0.0165 | 0.0326 | 0.2594 | -0.0185 | 0.2507 | 28.7912 | 58.1966 | 84.0861 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resseq 1:17)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 18:28)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 29:44)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 45:62)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 63:80)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 81:93)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 94:111)8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resseq 112:126)9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resseq 127:141)10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resseq 142:166)11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resseq 167:183)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 1:17)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 18:28)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 29:44)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 45:62)16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resseq 63:90)17 | X-RAY DIFFRACTION | 17 | chain 'B' and (resseq 91:100)18 | X-RAY DIFFRACTION | 18 | chain 'B' and ( | | | | | | | | | | | | | | | | | |
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