Software | Name | Version | Classification |
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PHASER | | phasingPHENIX | (phenix.refine: 1.8.2_1309)refinementXDS | | data reductionXDS | | data scaling | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.339 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.93 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1957 | 2000 | 3.57 % |
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Rwork | 0.1827 | - | - |
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obs | 0.1832 | 56021 | 99.5 % |
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 1.4→40.339 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2063 | 0 | 87 | 236 | 2386 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.015 | 2367 | X-RAY DIFFRACTION | f_angle_d1.787 | 3229 | X-RAY DIFFRACTION | f_dihedral_angle_d18.667 | 899 | X-RAY DIFFRACTION | f_chiral_restr0.092 | 354 | X-RAY DIFFRACTION | f_plane_restr0.008 | 429 | | | | | |
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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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1.4-1.435 | 0.3358 | 138 | 0.3503 | 3708 | X-RAY DIFFRACTION | 98 | 1.435-1.4738 | 0.3494 | 138 | 0.3106 | 3730 | X-RAY DIFFRACTION | 98 | 1.4738-1.5172 | 0.2877 | 141 | 0.2717 | 3827 | X-RAY DIFFRACTION | 99 | 1.5172-1.5662 | 0.2285 | 139 | 0.2221 | 3770 | X-RAY DIFFRACTION | 99 | 1.5662-1.6221 | 0.2569 | 143 | 0.2168 | 3839 | X-RAY DIFFRACTION | 100 | 1.6221-1.6871 | 0.2077 | 141 | 0.2091 | 3831 | X-RAY DIFFRACTION | 100 | 1.6871-1.7639 | 0.2276 | 143 | 0.1933 | 3842 | X-RAY DIFFRACTION | 100 | 1.7639-1.8569 | 0.2019 | 142 | 0.1849 | 3855 | X-RAY DIFFRACTION | 100 | 1.8569-1.9732 | 0.1697 | 144 | 0.1722 | 3870 | X-RAY DIFFRACTION | 100 | 1.9732-2.1255 | 0.1988 | 143 | 0.16 | 3868 | X-RAY DIFFRACTION | 100 | 2.1255-2.3394 | 0.1644 | 144 | 0.1608 | 3893 | X-RAY DIFFRACTION | 100 | 2.3394-2.6779 | 0.1942 | 145 | 0.1718 | 3913 | X-RAY DIFFRACTION | 100 | 2.6779-3.3736 | 0.194 | 146 | 0.1731 | 3946 | X-RAY DIFFRACTION | 100 | 3.3736-40.3557 | 0.1721 | 153 | 0.1721 | 4129 | 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 | 6.7964 | 6.0582 | 1.8149 | 5.6038 | 0.4029 | 4.961 | 0.2071 | -0.2842 | -0.225 | -0.0642 | -0.1769 | -0.174 | 0.5154 | 0.1715 | -0.0292 | 0.227 | 0.0495 | 0.0008 | 0.096 | -0.0546 | 0.1815 | 14.2489 | 11.5089 | 18.0467 | 2 | 2.1821 | -7.4973 | 7.9068 | 6.9524 | -3.4715 | 9.3833 | 0.3409 | -0.2312 | -0.8743 | -0.5173 | -0.0329 | 0.6785 | 0.0669 | -0.1336 | -0.2841 | 0.2028 | -0.0698 | -0.0492 | 0.069 | 0.0468 | 0.2317 | 5.6869 | 18.4716 | 3.5674 | 3 | 2.3077 | -0.3857 | 0.3868 | 5.6096 | -2.7935 | 7.5873 | 0.0438 | -0.0119 | 0.1107 | 0.0316 | 0.1208 | 0.3869 | -0.3162 | -0.2839 | -0.1636 | 0.1761 | -0.0163 | 0.034 | 0.0748 | -0.0209 | 0.1129 | 4.8235 | 23.6538 | 14.3813 | 4 | 1.1771 | 0.4265 | -2.2893 | 9.7673 | 1.7674 | 2.0169 | 0.1387 | -0.1553 | -0.3784 | -0.1165 | -0.1543 | 0.0483 | -0.822 | 0.7334 | -0.0886 | 0.1857 | -0.0071 | 0.0421 | 0.0828 | -0.0369 | 0.0737 | 6.4188 | 27.1339 | 19.445 | 5 | 0.9542 | 1.8043 | -1.9107 | 4.2716 | -5.6782 | 9.7534 | -0.1349 | 0.0817 | 0.0335 | 0.0773 | 0.112 | 0.0696 | -0.6631 | 0.0998 | 0.1905 | 0.3864 | -0.0374 | 0.0747 | 0.1494 | -0.0162 | 0.1554 | 7.4429 | 32.0518 | 15.8262 | 6 | 7.2425 | -1.8689 | 4.3451 | 6.2721 | 0.0788 | 5.6401 | 0.6248 | 0.3728 | -0.1454 | -0.7337 | -0.321 | 0.2578 | 0.312 | 0.1601 | -0.2597 | 0.2586 | -0.013 | -0.0063 | 0.1284 | 0.0029 | 0.112 | 10.9395 | 22.2531 | 2.1179 | 7 | 6.2308 | -2.5007 | 0.5061 | 8.0642 | -0.1076 | 2.0256 | 0.0113 | -0.3687 | 0.1535 | 0.4151 | 0.2112 | -0.5267 | -0.5463 | 0.5847 | -0.1767 | 0.1891 | -0.0949 | -0.0033 | 0.1969 | -0.0074 | 0.1501 | 20.4875 | 23.8004 | 15.7663 | 8 | 3.9496 | 0.8049 | -2.2513 | 3.6967 | 4.929 | 9.7368 | 0.1066 | 0.1352 | 0.14 | -0.2502 | -0.0428 | -0.0834 | -1.0458 | 0.1585 | -0.2456 | 0.2776 | -0.0601 | 0.0502 | 0.1403 | -0.0092 | 0.1341 | 16.5516 | 28.1006 | 8.7833 | 9 | 1.2811 | -1.0654 | -0.8455 | 6.8958 | -0.6606 | 2.3366 | -0.1785 | -0.0696 | -0.0424 | 0.3393 | 0.2331 | -0.1748 | -0.4103 | 0.4253 | -0.0162 | 0.2257 | -0.0186 | 0.009 | 0.1377 | -0.0131 | 0.085 | 12.2032 | 18.0432 | 21.6542 | 10 | 2.0718 | -1.3259 | 5.0913 | 3.866 | -3.729 | 7.0721 | -0.0183 | 0.4582 | -0.1539 | 0.0792 | 0.0247 | 0.152 | 0.0548 | 0.3379 | -0.0383 | 0.2086 | -0.0203 | -0.013 | 0.1095 | -0.0197 | 0.2052 | 11.1321 | 12.1034 | 6.8565 | 11 | 4.4902 | 1.8264 | 0.7499 | 3.6202 | 3.3089 | 3.9225 | 0.1752 | -0.075 | 0.2515 | 0.0253 | -0.0628 | -0.1613 | -0.1035 | -0.2223 | -0.132 | 0.1986 | -0.0118 | -0.0269 | 0.0601 | 0.0227 | 0.1301 | 4.6473 | 2.7602 | 10.8307 | 12 | 6.5627 | -2.5842 | 1.1786 | 6.3312 | -4.1489 | 3.8329 | -0.0048 | -0.2317 | 0.2596 | 0.4623 | -0.1987 | -1.1732 | -0.1253 | 0.5153 | 0.2212 | 0.1854 | -0.0115 | -0.1173 | 0.1557 | -0.059 | 0.3161 | 21.8331 | -2.6511 | 12.4424 | 13 | 6.8582 | -3.1275 | -1.3953 | 3.4522 | 0.5212 | 2.284 | 0.0113 | -0.1901 | 0.204 | 0.2079 | 0.0516 | -0.0949 | -0.0402 | 0.0171 | -0.0726 | 0.1477 | -0.0237 | 0.0118 | 0.0728 | -0.0149 | 0.0825 | 8.1292 | -7.0369 | 15.9043 | 14 | 9.6773 | 7.8054 | -1.2581 | 2.0391 | 1.9615 | 8.1711 | 0.3824 | -1.0383 | -1.06 | 0.9575 | -0.0979 | -0.8503 | 0.6576 | 0.4858 | -0.1715 | 0.2663 | 0.059 | -0.0789 | 0.2912 | 0.0614 | 0.3064 | 21.8641 | -16.7548 | 18.6854 | 15 | 2.8046 | -3.2975 | -5.3225 | 5.8063 | 2.5261 | 4.6889 | -0.0986 | -0.1174 | -0.1391 | 0.2804 | 0.0106 | -0.0158 | 0.1835 | 0.1154 | 0.1793 | 0.1669 | -0.0159 | -0.0011 | 0.1401 | -0.0008 | 0.0668 | 8.5129 | -15.8731 | 15.7512 | 16 | 6.1666 | 1.2731 | 3.463 | 6.1331 | -0.3146 | 3.5198 | -0.1907 | 0.126 | 0.9646 | -0.158 | -0.0764 | -1.2538 | 0.1427 | 0.3778 | 0.2434 | 0.1453 | 0.0323 | -0.0001 | 0.1767 | -0.0339 | 0.308 | 21.3642 | -6.7076 | 7.3799 | 17 | 7.1879 | -1.9704 | 0.8292 | 8.8345 | -1.9577 | 5.4268 | -0.1236 | 0.1973 | -0.0042 | -0.5981 | 0.1897 | 0.1887 | 0.1653 | -0.3044 | -0.0559 | 0.1802 | -0.0253 | -0.01 | 0.1054 | -0.0054 | 0.0667 | 4.1176 | -9.4323 | 2.9934 | 18 | 1.9937 | 3.3513 | 1.635 | 5.4331 | -1.5981 | 1.8812 | 0.0122 | 0.4582 | 0.1173 | -0.4361 | 0.0972 | -0.2583 | 0.1761 | 0.1103 | 0.0922 | 0.1902 | 0.0153 | 0.0389 | 0.1077 | -0.04 | 0.1334 | 13.8425 | -12.7601 | 3.3604 | 19 | 3.6708 | -0.6582 | 1.9548 | 6.1566 | -0.0877 | 5.3404 | -0.2093 | 0.0569 | 0.1135 | -0.0816 | 0.1242 | 0.2553 | -0.1934 | -0.0071 | 0.0723 | 0.0837 | -0.0065 | 0.0433 | 0.0842 | -0.0025 | 0.0213 | 2.4613 | -5.3915 | 12.8235 | 20 | 6.786 | -6.6703 | 5.9607 | 9.5176 | -8.5973 | 8.0507 | 0.4596 | 0.1143 | -0.4297 | 0.104 | -0.0569 | -0.0606 | 0.4979 | 0.1613 | -0.4835 | 0.2377 | 0.0014 | -0.0277 | 0.1219 | -0.038 | 0.1754 | 15.9777 | 2.9583 | 9.3321 |
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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 (resid 2 through 15 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 17 through 29 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 30 through 56 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 57 through 66 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 67 through 76 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 77 through 89 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 90 through 99 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 100 through 109 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 110 through 124 )10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 125 through 134 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 2 through 15 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 17 through 29 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 30 through 48 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 49 through 56 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 57 through 76 )16 | X-RAY DIFFRACTION | 16 | chain 'B' | | | | | | | | | | | | | | | |
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