Software | Name | Version | Classification |
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PHENIX | (1.13_2998: 000)refinement Coot | | model buildingXDS | | data scalingPHENIX | | phasingXDS | | data reduction | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 3.104→48.429 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 28.24
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2659 | 3056 | 9.89 % |
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Rwork | 0.2216 | - | - |
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obs | 0.226 | 16640 | 99 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Refinement step | Cycle: LAST / Resolution: 3.104→48.429 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6140 | 0 | 2 | 13 | 6155 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.01 | 6286 | X-RAY DIFFRACTION | f_angle_d1.107 | 8522 | X-RAY DIFFRACTION | f_dihedral_angle_d21.257 | 3836 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 949 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1091 | | | | | |
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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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3.1043-3.1528 | 0.3818 | 128 | 0.3484 | 1254 | X-RAY DIFFRACTION | 96 | 3.1528-3.2045 | 0.3419 | 132 | 0.3525 | 1264 | X-RAY DIFFRACTION | 100 | 3.2045-3.2597 | 0.3657 | 131 | 0.3186 | 1267 | X-RAY DIFFRACTION | 99 | 3.2597-3.319 | 0.3396 | 145 | 0.3262 | 1278 | X-RAY DIFFRACTION | 100 | 3.319-3.3828 | 0.3576 | 148 | 0.2994 | 1262 | X-RAY DIFFRACTION | 100 | 3.3828-3.4518 | 0.2906 | 133 | 0.2777 | 1290 | X-RAY DIFFRACTION | 100 | 3.4518-3.5269 | 0.3419 | 155 | 0.2786 | 1278 | X-RAY DIFFRACTION | 100 | 3.5269-3.6089 | 0.3533 | 121 | 0.2546 | 1251 | X-RAY DIFFRACTION | 100 | 3.6089-3.6991 | 0.2864 | 151 | 0.2409 | 1317 | X-RAY DIFFRACTION | 100 | 3.6991-3.7991 | 0.2841 | 132 | 0.2271 | 1244 | X-RAY DIFFRACTION | 100 | 3.7991-3.9108 | 0.2803 | 141 | 0.2251 | 1272 | X-RAY DIFFRACTION | 99 | 3.9108-4.037 | 0.3127 | 139 | 0.2128 | 1280 | X-RAY DIFFRACTION | 100 | 4.037-4.1812 | 0.2483 | 136 | 0.2079 | 1264 | X-RAY DIFFRACTION | 99 | 4.1812-4.3485 | 0.2588 | 148 | 0.2025 | 1257 | X-RAY DIFFRACTION | 99 | 4.3485-4.5463 | 0.2161 | 126 | 0.1859 | 1276 | X-RAY DIFFRACTION | 99 | 4.5463-4.7858 | 0.216 | 153 | 0.1662 | 1258 | X-RAY DIFFRACTION | 99 | 4.7858-5.0853 | 0.1994 | 123 | 0.1732 | 1272 | X-RAY DIFFRACTION | 99 | 5.0853-5.4775 | 0.2396 | 145 | 0.1997 | 1278 | X-RAY DIFFRACTION | 99 | 5.4775-6.0278 | 0.2801 | 139 | 0.1977 | 1246 | X-RAY DIFFRACTION | 99 | 6.0278-6.8979 | 0.2418 | 138 | 0.2166 | 1271 | X-RAY DIFFRACTION | 99 | 6.8979-8.6824 | 0.231 | 133 | 0.1875 | 1270 | X-RAY DIFFRACTION | 99 | 8.6824-48.4348 | 0.2062 | 159 | 0.1834 | 1197 | X-RAY DIFFRACTION | 96 |
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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 | 4.4037 | -1.6499 | -2.7489 | 4.8951 | 0.7539 | 8.9561 | 0.0068 | -1.1057 | 0.2277 | 1.1807 | -0.1966 | -0.3555 | 0.2612 | 1.0236 | 0.0102 | 0.7515 | -0.1238 | -0.1047 | 1.0782 | 0.1686 | 0.3306 | 108.6843 | 3.9709 | -57.0972 | 2 | 3.6408 | -2.4171 | -2.793 | 4.1881 | 1.6816 | 7.8071 | -0.2412 | -0.7171 | -0.1145 | 0.2212 | -0.0086 | -0.2166 | -0.5749 | 0.9887 | 0.2605 | 0.68 | -0.0088 | -0.1676 | 0.684 | 0.1351 | 0.5027 | 107.0989 | 2.8447 | -54.0225 | 3 | 8.2304 | 0.7287 | -3.554 | 4.0437 | 0.5417 | 7.9579 | 0.0068 | 1.3314 | -0.1786 | 0.0243 | 0.0917 | -0.53 | 0.1014 | 0.9624 | 0.002 | 0.7586 | -0.0378 | 0.0732 | 0.7942 | -0.0462 | 0.3427 | 111.0411 | 4.6612 | -70.6742 | 4 | 1.8811 | 0.4848 | 0.2299 | 3.2422 | -1.5544 | 0.8509 | -0.502 | -0.1493 | 0.2702 | 0.0648 | 0.3908 | 0.444 | -0.7481 | -0.2615 | 0.053 | 1.4035 | 0.038 | -0.2764 | 0.7374 | 0.1418 | 0.7629 | 107.2944 | 17.0802 | -67.3269 | 5 | 4.2895 | -1.1929 | -5.0866 | 3.4101 | 2.0936 | 6.1576 | 0.6084 | 0.0223 | 0.8308 | 0.4081 | 1.4586 | -0.9164 | -0.0378 | 1.1334 | -2.0232 | 0.8064 | -0.1991 | 0.0131 | 0.8197 | -0.1589 | 0.8512 | 116.5721 | 21.0993 | -68.6698 | 6 | 5.2303 | 2.2288 | -6.6344 | 7.1328 | -4.0133 | 8.6148 | 0.0748 | 0.0421 | -0.9215 | 0.7065 | -0.868 | -0.8691 | -1.0167 | 1.362 | 0.4229 | 0.7155 | -0.3529 | -0.0779 | 0.6775 | -0.0556 | 0.6595 | 120.0404 | 11.9659 | -71.0518 | 7 | 6.5113 | 5.5946 | -7.0453 | 9.6838 | -4.5352 | 8.1757 | 1.1759 | -0.7908 | -0.2258 | 0.724 | 0.3732 | 0.2268 | -2.2231 | 0.6925 | -1.1247 | 1.246 | -0.3755 | -0.1837 | 0.8995 | 0.1418 | 0.5162 | 113.313 | 14.3954 | -60.5852 | 8 | 2.0566 | 3.0032 | -2.9527 | 3.1215 | -1.5398 | 8.6557 | 0.3592 | 1.6364 | -1.2336 | 0.5111 | 0.1967 | -0.2964 | -0.5213 | -0.0019 | -0.1198 | 0.5403 | -0.1167 | 0.0568 | 0.6511 | 0.1077 | 0.3926 | 100.9087 | 5.6681 | -62.1996 | 9 | 8.8802 | 2.3324 | -4.1172 | 6.3899 | 2.118 | 9.6007 | 0.6559 | 1.3401 | 1.3898 | 1.1115 | 0.2452 | 0.6724 | -1.4928 | -1.4759 | -0.6763 | 0.7757 | -0.0784 | 0.1895 | 0.5216 | 0.3617 | 0.4795 | 93.5952 | 6.5779 | -57.9283 | 10 | 8.0384 | 0.8801 | 8.2051 | 5.4711 | 0.7209 | 8.7548 | 0.15 | -1.3259 | -1.2347 | -0.145 | 0.2048 | 0.3601 | -0.1618 | -0.33 | -0.0575 | 0.5689 | -0.0649 | 0.1943 | 0.7623 | 0.0653 | 0.4406 | 82.6646 | -4.4792 | -68.1617 | 11 | 6.695 | -3.4844 | -2.1257 | 7.8796 | 2.0766 | 4.5049 | -0.1364 | -0.2946 | 0.0594 | 0.0748 | -0.0248 | 0.1899 | -0.0913 | -0.1023 | 0.0168 | 0.2188 | -0.0918 | 0.0452 | 0.4482 | -0.016 | 0.2518 | 90.5853 | 6.6869 | -79.3974 | 12 | 1.8388 | -1.8169 | -0.6932 | 6.5804 | 2.507 | 7.916 | -0.1909 | 0.9787 | -1.2238 | -0.3049 | 0.346 | 0.0714 | 0.7847 | 0.2406 | -0.1764 | 0.5301 | -0.1179 | 0.076 | 0.816 | -0.2962 | 0.7215 | 94.3516 | -6.2276 | -96.1901 | 13 | 5.3567 | 0.8759 | 0.7546 | 5.5872 | -0.2491 | 5.5516 | -0.4171 | 0.2584 | -0.2821 | -0.4339 | 0.7658 | -0.4524 | 0.0899 | 1.0276 | -0.3213 | 0.4114 | -0.0293 | 0.0488 | 0.7632 | -0.1217 | 0.2942 | 106.2705 | 2.1127 | -85.2723 | 14 | 4.699 | 1.1489 | -1.9403 | 4.3791 | -0.7305 | 5.0419 | -0.0922 | 0.6302 | 0.417 | -0.3787 | 0.1841 | 0.5139 | -0.3977 | -0.5478 | 0.0118 | 0.2885 | -0.0366 | -0.0985 | 0.3822 | -0.0656 | 0.3113 | 86.7208 | 11.9501 | -86.5342 | 15 | 7.9929 | -2.1608 | -2.5767 | 3.8385 | -0.5699 | 6.5111 | 0.1776 | -1.0176 | -0.3536 | 0.9997 | -0.8378 | -1.0206 | -0.3802 | 0.8644 | -0.2018 | 0.6462 | -0.2107 | -0.1749 | 1.1256 | 0.2332 | 0.486 | 109.0514 | 46.7847 | -5.5265 | 16 | 5.4681 | -1.5985 | -1.4971 | 3.8165 | -0.0489 | 5.7858 | 0.2832 | -1.7969 | -0.1254 | 0.9197 | -0.3095 | -0.2707 | -0.3428 | 1.1256 | -0.0658 | 0.7601 | -0.1865 | -0.0782 | 1.1307 | 0.1396 | 0.4282 | 107.2994 | 45.9915 | -2.3735 | 17 | 5.6778 | -0.5207 | 1.4545 | 6.4599 | 1.3171 | 2.5072 | 0.4653 | -0.2305 | -1.694 | 1.5012 | -0.0002 | 0.4293 | 0.8609 | 0.4387 | -0.2301 | 0.7706 | 0.0786 | -0.0744 | 0.3083 | -0.0847 | 0.4527 | 112.2038 | 46.7662 | -19.0056 | 18 | 5.3485 | 2.2354 | 2.386 | 4.6455 | -0.4535 | 4.1043 | 0.5065 | 1.3881 | 1.1891 | 0.7916 | 0.4264 | 1.6512 | -1.7349 | -0.2386 | -0.9451 | 0.8603 | 0.1545 | 0.161 | 1.3407 | 0.2768 | 0.4743 | 106.1821 | 56.3838 | -18.9108 | 19 | 6.2384 | 5.4391 | -1.7102 | 2.0003 | -4.1134 | 1.9915 | 0.7932 | -1.2179 | 1.1784 | 2.5389 | -0.0969 | 0.1094 | -2.8017 | -0.3492 | -0.8048 | 1.3066 | -0.1305 | 0.1179 | 0.7115 | -0.0371 | 0.6162 | 117.5687 | 65.7845 | -11.7257 | 20 | 3.9924 | 4.5677 | -1.5106 | 9.7253 | -4.3782 | 8.7636 | 0.3176 | -0.2392 | 0.7626 | 0.7114 | 0.2824 | -0.4559 | -0.7711 | -0.2323 | -0.6455 | 0.3684 | -0.0377 | 0.0425 | 0.7126 | -0.1065 | 0.5132 | 117.6242 | 57.5677 | -17.4988 | 21 | 6.1025 | 2.87 | 4.1983 | 5.5708 | 1.1384 | 2.994 | 0.2476 | 0.6044 | -0.1221 | -0.194 | 0.0108 | 0.0536 | -0.4387 | -0.2906 | -0.2585 | 0.6001 | -0.0695 | 0.1353 | 0.9515 | -0.0201 | 0.338 | 94.107 | 46.4519 | -11.4115 | 22 | 5.3645 | -2.7742 | -2.605 | 5.2632 | -0.7845 | 7.4167 | -0.3308 | 0.4369 | -0.1171 | 0.2765 | -0.0591 | 0.185 | -0.5352 | 0.6359 | 0.2775 | 0.3446 | -0.1057 | 0.0021 | 0.6264 | 0.0207 | 0.3256 | 90.7656 | 49.8661 | -27.5199 | 23 | 3.9803 | 0.6682 | -1.7136 | 0.7802 | -2.0824 | 7.5532 | -1.167 | 1.153 | -1.5471 | -0.0438 | -1.2068 | -0.0417 | 1.7541 | -0.0391 | 1.062 | 0.6614 | -0.1517 | -0.1821 | 1.5619 | -0.5433 | 0.4795 | 94.6325 | 34.6741 | -44.4862 | 24 | 6.0147 | 1.3515 | -1.053 | 3.7731 | 0.5216 | 5.2318 | -0.124 | 0.4515 | -0.5929 | -0.0832 | 0.1304 | -0.0808 | -0.1012 | 0.0986 | -0.0231 | 0.3503 | 0 | -0.0464 | 0.5005 | -0.0287 | 0.2843 | 100.6248 | 43.4628 | -30.2956 | 25 | 4.8107 | 0.3431 | -1.1426 | 4.8419 | 1.4233 | 3.8394 | -0.0874 | 1.2016 | 0.7318 | -0.8863 | -0.1626 | 0.3655 | -0.9217 | -0.5015 | 0.2371 | 0.5184 | 0.0748 | -0.1428 | 0.9918 | 0.0631 | 0.5161 | 87.5829 | 58.5478 | -40.3887 |
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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 0 through 10 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 11 through 38 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 39 through 48 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 49 through 60 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 61 through 75 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 76 through 85 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 86 through 93 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 94 through 106 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 107 through 113 )10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 114 through 124 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 23 through 63 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 64 through 110 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 111 through 187 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 188 through 293 )15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resid 0 through 10 )16 | X-RAY DIFFRACTION | 16 | chain 'C' | | | | | | | | | | | | | | | |
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