Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE)refinementXDS | | data reductionXDS | | data scalingPHENIX | AUTOSOLphasing | | | | | |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2.7→39.92 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 29.68 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.241 | 744 | 4.7 % |
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Rwork | 0.2031 | - | - |
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obs | 0.2049 | 15882 | 99.87 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 91.6 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.7→39.92 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2062 | 0 | 0 | 13 | 2075 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.005 | 2124 | X-RAY DIFFRACTION | f_angle_d0.994 | 2869 | X-RAY DIFFRACTION | f_dihedral_angle_d12.844 | 810 | X-RAY DIFFRACTION | f_chiral_restr0.074 | 326 | X-RAY DIFFRACTION | f_plane_restr0.006 | 381 | | | | | |
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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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2.7003-2.9087 | 0.3966 | 160 | 0.3338 | 3040 | X-RAY DIFFRACTION | 100 | 2.9087-3.2013 | 0.3214 | 168 | 0.253 | 3007 | X-RAY DIFFRACTION | 100 | 3.2013-3.6643 | 0.2598 | 148 | 0.2176 | 3017 | X-RAY DIFFRACTION | 100 | 3.6643-4.6155 | 0.207 | 128 | 0.1833 | 3040 | X-RAY DIFFRACTION | 100 | 4.6155-39.9243 | 0.2131 | 140 | 0.185 | 3034 | 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 | 6.2521 | -4.0653 | -0.7005 | 8.1786 | -1.6263 | 8.2038 | -0.5372 | -1.3843 | -0.2886 | 1.0433 | -0.0854 | -1.1207 | -0.8021 | 0.4286 | 0.7325 | 0.9484 | -0.2441 | -0.3095 | 0.803 | -0.0523 | 0.5916 | 47.3067 | 16.123 | 33.0166 | 2 | 2.7987 | -0.469 | 3.244 | 1.3843 | 0.6574 | 5.1202 | 0.7793 | -0.6097 | -1.0725 | 0.6145 | 0.2402 | -1.6913 | 0.3259 | 0.9829 | -0.7474 | 0.8435 | 0.1039 | -0.2096 | 0.5507 | -0.1823 | 0.7642 | 42.1568 | 6.6323 | 15.6972 | 3 | 4.7007 | -0.1531 | 4.5089 | 0.1192 | -0.2779 | 4.4767 | 0.2644 | -1.4708 | -1.245 | 3.0508 | -0.3979 | 0.7524 | 2.027 | -0.5449 | -0.1476 | 1.5859 | -0.2368 | 0.27 | 0.8006 | 0.0706 | 0.743 | 31.2686 | 7.7741 | 31.7164 | 4 | 4.3924 | 2.2692 | 3.5213 | 4.5394 | 0.1325 | 3.6713 | 0.8673 | -0.9227 | -1.9877 | 2.3915 | -0.1836 | 0.4327 | 1.876 | 0.3846 | -0.3397 | 1.0462 | 0.0764 | -0.0563 | 0.4292 | -0.0364 | 0.9788 | 36.5137 | 4.1818 | 30.4418 | 5 | 7.7343 | 6.3532 | -6.8745 | 5.6006 | -5.1709 | 6.7081 | -0.8311 | -0.0589 | -1.9878 | 1.2501 | -0.7006 | -3.5214 | 1.0394 | 0.069 | 1.3566 | 0.8304 | 0.1543 | -0.309 | 0.6759 | -0.1762 | 1.2527 | 43.6355 | -2.4868 | 20.3256 | 6 | 2.0011 | -2.2844 | 3.2113 | 8.8639 | -1.9456 | 4.536 | -0.5512 | -1.2326 | -1.5034 | 1.5449 | -0.2411 | -0.4442 | 1.2812 | 0.0329 | -0.0425 | 1.1541 | 0.177 | -0.2288 | 0.5195 | -0.0952 | 0.7077 | 45.446 | 5.4805 | 26.7922 | 7 | 3.9209 | -0.9097 | 0.1798 | 6.0974 | 0.0818 | 5.5971 | 0.167 | 0.5688 | -0.9963 | 0.0634 | -0.1986 | 1.033 | 1.0189 | -0.3006 | -0.1437 | 0.6768 | -0.1363 | -0.04 | 0.3908 | -0.1871 | 0.6251 | 30.7873 | 12.032 | 15.0985 | 8 | 8.9633 | 2.2762 | -5.8307 | 7.3199 | -2.4034 | 5.5648 | -0.5845 | 1.0351 | -1.0373 | 0.2766 | -0.4475 | 0.959 | -0.086 | -1.6365 | 1.0825 | 0.8638 | -0.063 | 0.347 | 0.5741 | -0.2907 | 0.9115 | 23.9611 | 18.2943 | 22.638 | 9 | 6.8376 | -1.3866 | 4.5514 | 1.8892 | 1.7521 | 7.4712 | 0.1675 | 1.2145 | 0.6869 | 0.3779 | -0.9735 | -0.14 | -0.703 | 0.7318 | 0.071 | 0.7854 | 0.1645 | -0.0112 | 0.4839 | 0.0421 | 0.5142 | 33.1057 | 29.2874 | 5.9956 | 10 | 2.9912 | 2.7379 | 1.2917 | 2.7319 | 1.2052 | 0.5594 | -0.2699 | 1.2717 | 0.1496 | -1.27 | -0.6247 | -0.474 | 0.0342 | -0.5569 | 0.1859 | 0.9691 | 0.1106 | 0.1325 | 0.7466 | 0.0596 | 0.4533 | 37.0132 | 30.0908 | 4.2729 | 11 | 6.1352 | 3.4509 | 4.8749 | 6.0194 | 3.2897 | 3.9464 | -0.161 | -0.1761 | 1.2512 | 1.9311 | 0.5139 | 2.415 | -0.16 | -0.8821 | -0.2572 | 0.487 | 0.014 | 0.2275 | 0.4595 | 0.0058 | 0.7178 | 25.8265 | 25.9917 | 21.6011 | 12 | 3.841 | 1.0152 | 2.6755 | 3.0303 | -2.2947 | 5.3372 | -0.0796 | 0.0931 | -0.318 | -1.5642 | -0.4681 | 1.0614 | 0.1898 | -1.0968 | 0.5926 | 0.6751 | 0.0018 | -0.1568 | 0.6065 | -0.2045 | 0.7336 | 26.3147 | 17.0615 | 5.278 | 13 | 0.8262 | -1.5844 | -1.3402 | 6.2222 | 4.5829 | 3.5894 | 1.4625 | -1.7906 | 0.6148 | 2.3979 | -2.1654 | -0.5676 | 0.0477 | -3.095 | 1.0446 | 1.2967 | 0.2683 | -0.3367 | 1.7955 | -0.3723 | 1.4292 | 15.8441 | 25.519 | 9.2758 | 14 | 0.3705 | -1.5778 | 1.6789 | 6.7275 | -7.152 | 7.6034 | 1.6001 | -1.9952 | 3.0106 | 2.6968 | 1.2244 | 2.2503 | -1.2985 | -2.3374 | -2.4811 | 1.2618 | 0.4742 | 0.2467 | 1.4951 | -0.3041 | 1.1683 | 22.6252 | 30.1176 | 13.9439 | 15 | 5.3816 | -0.204 | 0.9001 | 6.7767 | -0.9251 | 5.8578 | 0.0362 | -0.4045 | -0.7394 | 0.4658 | -0.1952 | 0.2488 | 0.7559 | 0.0254 | 0.1062 | 0.5789 | -0.049 | 0.1049 | 0.2505 | -0.0155 | 0.3929 | 34.3087 | 12.9114 | 21.6824 | 16 | 6.9788 | 1.4887 | 6.7293 | 8.7687 | -0.4517 | 7.4872 | 0.1514 | -2.5514 | -0.3738 | 0.9459 | -0.2422 | 0.806 | 2.0736 | -0.5279 | -0.0964 | 1.2243 | -0.2146 | -0.0132 | 1.0814 | 0.5621 | 0.8368 | -8.9769 | 2.4563 | 16.5174 | 17 | 2.0381 | -2.5176 | 1.0947 | 9.5526 | -5.5662 | 3.3438 | 0.4991 | 0.7205 | -0.5882 | -1.3335 | -1.1941 | 0.3992 | 1.6745 | 0.756 | 0.1308 | 0.6191 | -0.1413 | -0.1342 | 0.7927 | 0.1914 | 0.7145 | -6.9069 | 6.579 | 1.1187 | 18 | 1.7023 | 1.9413 | -0.7381 | 8.458 | 3.4738 | 5.8968 | 1.2585 | -0.9883 | 1.2407 | -0.9881 | -0.2176 | -0.4466 | 0.3779 | 0.0369 | -1.1132 | 0.5355 | -0.0896 | -0.0476 | 0.6457 | 0.169 | 1.0239 | -4.3733 | 17.1152 | -2.0916 | 19 | 0.2468 | 0.1598 | -0.0472 | 0.2697 | -0.0877 | 0.0289 | 0.2921 | -1.2955 | 1.0336 | 1.7761 | -0.4645 | -0.6977 | -1.5156 | 1.8698 | 0.9467 | 0.9007 | -0.2037 | -0.2207 | 1.194 | 0.0643 | 1.1242 | -1.1181 | 20.5565 | 9.4795 | 20 | 3.7372 | -4.5653 | 3.1497 | 6.751 | -4.7609 | 3.3654 | -0.7662 | -2.5282 | 0.5559 | 3.4849 | -0.1792 | -1.236 | -0.4291 | 0.5964 | 0.9795 | 1.0796 | 0.223 | -0.1965 | 1.3871 | -0.0156 | 0.9398 | 5.9493 | 12.9057 | 17.7645 | 21 | 2.0009 | -8.9555 | 7.9212 | 2.0006 | -6.4113 | 5.6423 | -0.4755 | -1.1048 | 0.4613 | 3.405 | 2.1614 | -0.2022 | -1.3348 | 0.4454 | 0.6629 | 1.3708 | 0.2227 | -0.0363 | 1.2932 | 0.314 | 0.972 | -4.4743 | 18.7659 | 12.5253 | 22 | 3.9148 | -4.0245 | 3.2937 | 4.3296 | -4.547 | 9.9071 | -0.3225 | 0.3384 | 0.9063 | 0.9483 | 0.388 | -0.1482 | -1.7432 | 0.9787 | -0.2898 | 0.8723 | -0.0964 | -0.1731 | 1.2651 | 0.0641 | 0.9173 | -9.0348 | 24.1845 | 2.2053 | 23 | 2.2449 | -2.6292 | 0.1414 | 6.0589 | -0.5336 | 0.0546 | -0.6095 | -0.5088 | -0.3802 | 0.8788 | 0.5397 | 0.4389 | -0.2164 | 0.4094 | -0.5328 | 0.8036 | 0.0881 | -0.6462 | 0.5585 | 0.2218 | 0.3724 | -2.9061 | 10.4691 | 5.6909 | 24 | 3.8004 | -2.6641 | 3.6477 | 3.3307 | -4.0444 | 5.5993 | 0.2855 | 0.9204 | 0.7228 | -0.7907 | -0.9378 | -0.392 | -0.341 | 0.58 | -1.2763 | 1.1115 | 0.0011 | -0.6657 | 0.74 | 0.4283 | 1.0245 | 4.6851 | 13.7624 | -11.8055 | 25 | 6.4906 | -1.7995 | -7.5768 | 0.4995 | 2.1006 | 8.8486 | 1.1134 | 0.4586 | 2.427 | -0.5089 | 0.7455 | -0.637 | -2.5603 | -0.1691 | -0.5277 | 0.8401 | -0.1292 | -0.0941 | 0.6755 | 0.4441 | 1.6686 | 13.0933 | 16.4192 | -5.4889 | 26 | 5.1615 | 1.0303 | -3.6201 | 3.6119 | -1.8416 | 2.9013 | -1.2662 | 0.4169 | 0.4796 | -1.3634 | -0.3625 | 0.6675 | -0.2911 | 0.7283 | -0.2305 | 0.7767 | -0.1814 | -0.4759 | 0.6989 | 0.1742 | 0.8289 | 11.2768 | 1.9263 | -4.7039 |
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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 14 THROUGH 23 )2 | X-RAY DIFFRACTION | 2 | CHAIN 'A' AND (RESID 24 THROUGH 31 )3 | X-RAY DIFFRACTION | 3 | CHAIN 'A' AND (RESID 32 THROUGH 40 )4 | X-RAY DIFFRACTION | 4 | CHAIN 'A' AND (RESID 41 THROUGH 47 )5 | X-RAY DIFFRACTION | 5 | CHAIN 'A' AND (RESID 48 THROUGH 56 )6 | X-RAY DIFFRACTION | 6 | CHAIN 'A' AND (RESID 57 THROUGH 61 )7 | X-RAY DIFFRACTION | 7 | CHAIN 'A' AND (RESID 62 THROUGH 87 )8 | X-RAY DIFFRACTION | 8 | CHAIN 'A' AND (RESID 88 THROUGH 92 )9 | X-RAY DIFFRACTION | 9 | CHAIN 'A' AND (RESID 93 THROUGH 103 )10 | X-RAY DIFFRACTION | 10 | CHAIN 'B' AND (RESID 14 THROUGH 23 )11 | X-RAY DIFFRACTION | 11 | CHAIN 'B' AND (RESID 24 THROUGH 28 )12 | X-RAY DIFFRACTION | 12 | CHAIN 'B' AND (RESID 29 THROUGH 44 )13 | X-RAY DIFFRACTION | 13 | CHAIN 'B' AND (RESID 45 THROUGH 51 )14 | X-RAY DIFFRACTION | 14 | CHAIN 'B' AND (RESID 52 THROUGH 60 )15 | X-RAY DIFFRACTION | 15 | CHAIN 'B' AND (RESID 61 THROUGH 104 )16 | X-RAY DIFFRACTION | 16 | CHAIN 'C' | | | | | | | | | | | | | | | |
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