Software | Name | Version | Classification | NB |
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DENZO | | data reduction | SCALEPACK | | data scaling | PHENIX | 1.7.1_743refinement | PDB_EXTRACT | 3.1 | data extraction | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KLY Resolution: 2.5→46.69 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.56 / σ(F): 1.36 / Phase error: 19.33 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.208 | 3144 | 5.07 % |
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Rwork | 0.162 | - | - |
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obs | 0.165 | 62054 | 99.8 % |
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Solvent computation | Shrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.87 Å2 / ksol: 0.32 e/Å3 |
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Displacement parameters | Biso mean: 56.63 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.3871 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 3.5148 Å2 | -0 Å2 |
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3- | - | - | 0.1533 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.5→46.69 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 9553 | 0 | 110 | 301 | 9964 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 9815 | X-RAY DIFFRACTION | f_angle_d0.996 | 13273 | X-RAY DIFFRACTION | f_dihedral_angle_d13.092 | 3441 | X-RAY DIFFRACTION | f_chiral_restr0.111 | 1665 | X-RAY DIFFRACTION | f_plane_restr0.003 | 1586 | | | | | |
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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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2.5022-2.5413 | 0.2361 | 128 | 0.1615 | 2603 | X-RAY DIFFRACTION | 96 | 2.5413-2.5829 | 0.2586 | 147 | 0.1606 | 2608 | X-RAY DIFFRACTION | 100 | 2.5829-2.6275 | 0.2444 | 145 | 0.1705 | 2674 | X-RAY DIFFRACTION | 100 | 2.6275-2.6752 | 0.2501 | 143 | 0.153 | 2628 | X-RAY DIFFRACTION | 100 | 2.6752-2.7267 | 0.2056 | 158 | 0.1472 | 2604 | X-RAY DIFFRACTION | 100 | 2.7267-2.7823 | 0.2152 | 134 | 0.1513 | 2691 | X-RAY DIFFRACTION | 100 | 2.7823-2.8428 | 0.2275 | 142 | 0.1555 | 2663 | X-RAY DIFFRACTION | 100 | 2.8428-2.9089 | 0.2273 | 153 | 0.1546 | 2646 | X-RAY DIFFRACTION | 100 | 2.9089-2.9817 | 0.2374 | 146 | 0.1513 | 2630 | X-RAY DIFFRACTION | 100 | 2.9817-3.0623 | 0.1898 | 136 | 0.149 | 2668 | X-RAY DIFFRACTION | 100 | 3.0623-3.1524 | 0.2035 | 143 | 0.1438 | 2679 | X-RAY DIFFRACTION | 100 | 3.1524-3.2541 | 0.1647 | 139 | 0.1452 | 2648 | X-RAY DIFFRACTION | 100 | 3.2541-3.3704 | 0.2167 | 157 | 0.1495 | 2684 | X-RAY DIFFRACTION | 100 | 3.3704-3.5053 | 0.2307 | 142 | 0.1588 | 2664 | X-RAY DIFFRACTION | 100 | 3.5053-3.6648 | 0.2033 | 127 | 0.1547 | 2703 | X-RAY DIFFRACTION | 100 | 3.6648-3.8579 | 0.2022 | 134 | 0.1497 | 2693 | X-RAY DIFFRACTION | 100 | 3.8579-4.0995 | 0.2008 | 135 | 0.1518 | 2703 | X-RAY DIFFRACTION | 100 | 4.0995-4.4158 | 0.1634 | 152 | 0.1442 | 2684 | X-RAY DIFFRACTION | 100 | 4.4158-4.8597 | 0.1919 | 123 | 0.1463 | 2720 | X-RAY DIFFRACTION | 100 | 4.8597-5.5619 | 0.2453 | 153 | 0.1688 | 2722 | X-RAY DIFFRACTION | 100 | 5.5619-7.0037 | 0.1951 | 155 | 0.1978 | 2763 | X-RAY DIFFRACTION | 100 | 7.0037-46.6984 | 0.2176 | 152 | 0.2008 | 2832 | X-RAY DIFFRACTION | 98 |
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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 | 2.1055 | 2.7472 | -1.2581 | 3.6597 | -1.9722 | 2.3187 | -0.0698 | -0.2706 | -0.0625 | 0.539 | 0.1758 | 0.9959 | 0.3226 | -0.2486 | -0.2107 | 0.7311 | 0.0526 | 0.3369 | 0.5165 | 0.071 | 0.4261 | -26.5729 | 24.972 | 10.0173 | 2 | 1.6867 | -0.3798 | 0.1053 | 4.1849 | -0.2604 | 2.2932 | -0.1693 | -0.086 | 0.1463 | 0.1396 | 0.1822 | -0.0977 | 0.1285 | -0.081 | -0.0033 | 0.2494 | 0.0356 | -0.012 | 0.275 | 0.0161 | 0.2526 | -9.0386 | 18.5743 | -6.9534 | 3 | 1.6738 | -0.0986 | -0.2759 | 2.082 | -0.8421 | 0.8769 | -0.0272 | -0.3043 | -0.0213 | 0.8922 | 0.0839 | 0.1267 | -0.0781 | -0.2145 | -0.0505 | 0.5335 | 0.016 | -0.0145 | 0.3771 | 0.106 | 0.274 | -13.3194 | 17.6458 | 8.8041 | 4 | 4.1553 | 3.1492 | 3.2795 | 3.1578 | 1.1164 | 5.0175 | -0.046 | 0.3814 | -0.3222 | -0.0567 | 0.1179 | -0.9117 | 0.2025 | 0.7814 | -0.0581 | 0.2391 | 0.0727 | -0.0479 | 0.3962 | 0.1316 | 0.491 | 6.5886 | 16.2183 | -6.9881 | 5 | 0.6159 | -0.4412 | 0.4604 | 2.8815 | 0.0233 | 1.2537 | -0.1504 | -0.2014 | -0.0921 | 0.5289 | 0.091 | -0.1719 | -0.0709 | -0.0476 | 0.0262 | 0.3331 | 0.0206 | -0.0259 | 0.3269 | 0.0485 | 0.2424 | -9.2847 | 26.5115 | -1.3866 | 6 | 7.7796 | 0.8054 | 0.4135 | 4.3811 | -4.2221 | 4.7932 | -0.7358 | -0.2039 | -0.7236 | -0.1222 | -0.2237 | -0.7287 | 0.0184 | 0.8191 | 0.7048 | 0.3342 | 0.0648 | -0.0281 | 0.5052 | 0.1213 | 0.6332 | 9.2837 | 9.4677 | -2.8775 | 7 | 4.3644 | -2.2376 | -0.7423 | 3.0636 | 1.0362 | 1.9879 | 0.0014 | -0.2587 | -0.1683 | 0.2503 | 0.1115 | -0.3793 | -0.3257 | 0.4521 | -0.1679 | 0.49 | 0.0079 | -0.1834 | 0.4559 | 0.0529 | 0.3273 | -1.3647 | 22.3225 | 8.7827 | 8 | 0.9996 | 2.3168 | -0.4879 | 5.7282 | 0.667 | 9.1668 | -0.102 | -1.1413 | 0.0036 | 0.6731 | 0.2994 | 0.6108 | -0.2571 | -0.3587 | -0.2081 | 0.6707 | 0.1594 | 0.1942 | 0.5395 | 0.0105 | 0.1904 | -20.1301 | 36.9024 | 12.4967 | 9 | 2.4812 | -0.4106 | 2.4796 | 1.6048 | -1.3792 | 8.6077 | 0.1143 | -0.5532 | -0.2185 | 0.3721 | 0.3773 | 0.3236 | -0.3881 | -1.2124 | -0.4277 | 0.4185 | 0.0927 | 0.2335 | 0.3735 | 0.0721 | 0.5444 | -32.0452 | 51.7598 | -1.543 | 10 | 2.5739 | -0.9982 | 0.2767 | 3.3841 | 0.0533 | 3.2085 | -0.0998 | -0.0473 | 0.2539 | 0.3154 | 0.0651 | -0.2486 | -0.0245 | 0.1122 | 0.0106 | 0.2167 | -0.0377 | -0.0526 | 0.1739 | 0.0129 | 0.2681 | -9.5897 | 41.3217 | -6.431 | 11 | 2.4841 | 1.9319 | 0.3356 | 1.5298 | 0.0632 | 4.0568 | -0.08 | -0.282 | 0.6639 | 0.8633 | 0.0489 | 0.405 | -0.3556 | -0.1835 | -0.0715 | 0.4352 | -0.0063 | 0.0836 | 0.3037 | -0.0363 | 0.3855 | -26.4048 | 57.6597 | -2.9492 | 12 | 4.025 | -1.3455 | 0.2279 | 2.086 | -0.3284 | 1.5856 | -0.1435 | -0.6452 | 0.511 | 0.6618 | 0.3097 | -0.1566 | -0.1935 | 0.1581 | -0.1771 | 0.5592 | -0.0581 | -0.0718 | 0.3241 | -0.0934 | 0.354 | -11.8547 | 50.7306 | 4.4199 | 13 | 1.135 | 0.0131 | -1.103 | 2.5045 | 0.1318 | 1.7679 | 0.0667 | 0.0596 | 0.2727 | 0.2414 | -0.173 | -1.2871 | -0.0933 | 0.4584 | 0.1786 | 0.2569 | -0.1253 | -0.1888 | 0.4526 | 0.0754 | 0.6658 | 5.2997 | 46.346 | -7.6866 | 14 | 1.2538 | -0.2729 | 0.655 | 2.8593 | -0.3101 | 1.8804 | -0.1419 | 0.0059 | 0.1398 | 0.3692 | 0.0504 | -0.0754 | -0.1855 | -0.1008 | 0.0619 | 0.3297 | 0.0157 | 0.011 | 0.3062 | 0.012 | 0.3184 | -13.9047 | 48.6051 | -11.1785 | 15 | 2.6848 | 0.6246 | 0.8213 | 0.1819 | 0.2134 | 1.6056 | 0.0991 | -0.1465 | -0.1921 | 0.1255 | -0.0502 | -0.289 | 0.0553 | 0.3191 | -0.0609 | 0.4184 | -0.0994 | -0.2976 | 0.9249 | -0.0396 | 1.0363 | 8.9363 | 48.9601 | -0.8874 | 16 | 6.465 | -0.5448 | 0.5308 | 4.3139 | -0.3155 | 3.0056 | -0.0117 | -0.1267 | 0.6954 | 0.637 | -0.2013 | -0.4572 | -0.7747 | 0.4589 | 0.1805 | 0.461 | -0.0782 | -0.0453 | 0.2607 | -0.0468 | 0.4232 | -7.9772 | 59.2173 | -4.9924 | 17 | 0.8833 | -1.4119 | 1.0426 | 5.7122 | 2.6206 | 6.5535 | 0.2199 | -0.4404 | 0.3724 | 0.214 | 0.105 | 0.838 | -0.4327 | -0.9226 | -0.1844 | 0.3329 | 0.1151 | 0.1906 | 0.2887 | 0.0922 | 0.546 | -31.0036 | 60.2697 | -12.5426 | 18 | 1.4022 | 0.3036 | 0.7118 | 0.4009 | 0.1586 | 1.0203 | -0.2727 | -0.1229 | 0.4674 | -0.2062 | 0.0674 | 0.3016 | -0.2418 | -0.3105 | -0.8867 | 0.5217 | -0.0936 | -0.6703 | 0.6889 | 0.0329 | 1.0255 | -43.9182 | 18.6231 | -34.2864 | 19 | 0.4713 | -0.3806 | 0.3787 | 1.8735 | -0.5511 | 1.2512 | 0.1248 | 0.8188 | -0.2798 | -1.5104 | -0.0319 | 0.9839 | 0.4253 | -0.3081 | 0.1521 | 0.4771 | -0.06 | -0.6047 | 0.3357 | -0.0835 | -0.5357 | -28.1102 | 27.0993 | -42.2545 | 20 | 2.2419 | 0.1957 | 0.1097 | 1.9869 | 1.7965 | 1.6361 | 0.1042 | 0.7026 | 0.2504 | -0.4028 | 0.4362 | -0.093 | -0.3707 | 0.172 | -0.2051 | 1.0117 | 0.044 | 0.1226 | 0.5538 | 0.053 | 0.1183 | -11.1124 | 29.858 | -50.407 | 21 | 2.532 | 1.1367 | 0.5074 | 1.1502 | 1.2553 | 3.4581 | 0.0383 | 0.3521 | -0.1675 | -0.8531 | 0.116 | 0.4846 | 0.3744 | -0.2404 | 0.0237 | 0.637 | -0.0642 | -0.1563 | 0.3525 | 0.0446 | 0.3535 | -24.7307 | 18.8667 | -34.0217 | 22 | 1.4546 | 0.7926 | 1.5121 | 6.6941 | -1.8585 | 4.2913 | -0.594 | 0.5142 | 0.0306 | -1.199 | 0.4224 | -0.4953 | -0.212 | 0.492 | 0.0108 | 1.2043 | -0.0592 | -0.0726 | 0.7162 | -0.0163 | 0.3639 | -18.4114 | 28.0931 | -51.685 | 23 | 0.3835 | -0.0794 | -0.2783 | 0.7755 | 0.1478 | 1.8208 | 0.1665 | 0.2112 | -0.2789 | -0.5406 | 0.073 | 0.1823 | 0.1749 | -0.1827 | 0.4922 | 1.0578 | -0.1803 | -0.5108 | 0.3804 | -0.245 | 0.3923 | -28.8189 | 13.3972 | -44.7867 | 24 | 4.1867 | 3.5088 | 1.1555 | 3.1749 | 1.7409 | 2.8645 | 0.0826 | 0.19 | -0.456 | 0.0255 | 0.157 | -0.3221 | 0.2454 | 0.1282 | -0.1461 | 0.6307 | -0.2286 | -0.4008 | 1.1538 | -0.1705 | 1.5848 | -45.5295 | -0.9041 | -30.9036 | 25 | 3.4799 | 1.6725 | 2.1942 | 5.9937 | 3.2532 | 7.5326 | -0.2361 | -0.1688 | 0.5664 | -0.1668 | -0.1456 | 1.6297 | 0.0259 | -1.2176 | 0.3985 | 0.3338 | -0.1484 | 0.0596 | 0.5157 | 0.1593 | 0.7822 | -33.7062 | 4.581 | -10.0338 | 26 | 2.0192 | 0.431 | 0.1946 | 3.4149 | -0.1094 | 2.573 | 0.0636 | 0.0189 | -0.3353 | -0.6521 | -0.0342 | 0.1035 | 0.539 | -0.0691 | 0.0392 | 0.3769 | 0.0286 | -0.0488 | 0.189 | -0.0275 | 0.2214 | -16.8622 | 11.9114 | -27.2214 | 27 | 2.7573 | -0.6029 | 0.0859 | 3.2764 | 2.4597 | 2.2265 | -0.3459 | -0.1557 | -1.0909 | 0.2355 | 0.0859 | 0.3524 | 0.7262 | -0.2121 | 0.2127 | 0.3651 | -0.0944 | 0.0026 | 0.4193 | 0.072 | 0.6919 | -27.1378 | -0.4362 | -9.8326 | 28 | 2.4055 | -1.0655 | -0.5539 | 0.484 | 0.0525 | 3.7967 | -0.0883 | -0.0208 | -0.5952 | -0.5259 | 0.0094 | 0.487 | 0.3354 | -0.5121 | 0.142 | 0.7848 | -0.0601 | -0.1017 | 0.2347 | -0.1378 | 0.467 | -22.6279 | -1.4626 | -26.9871 | 29 | 2.0785 | 0.6968 | 0.0219 | 0.9434 | -1.2721 | 2.3142 | 0.1459 | 0.1473 | -0.2645 | -0.87 | -0.3016 | -0.311 | 0.0713 | 0.3934 | 0.1609 | 0.8484 | 0.1357 | 0.2413 | 0.3567 | -0.0472 | 0.4874 | -3.5447 | 6.1101 | -33.4085 | 30 | 3.3554 | -1.2828 | -0.3974 | 3.5894 | 0.0799 | 3.2428 | 0.0367 | -0.0075 | -0.4368 | -0.1953 | -0.0258 | 0.5391 | 0.4154 | -0.0605 | -0.0348 | 0.3082 | -0.0113 | 0.0477 | 0.2373 | 0.0154 | 0.3446 | -14.1997 | 5.8202 | -12.9227 | 31 | 1.362 | -0.6398 | 0.4783 | 3.4793 | -1.0506 | 3.8752 | -0.094 | 0.1939 | -0.2175 | -0.0076 | 0.0709 | 0.5691 | -0.0719 | -0.6817 | 0.0029 | 0.1949 | -0.0494 | -0.0079 | 0.222 | -0.001 | 0.2708 | -19.2202 | 18.1636 | -15.6576 | 32 | 2.7386 | 0.2579 | 0.0873 | 1.8385 | -0.2204 | 2.8846 | -0.1841 | 0.4195 | -0.2907 | -1.0546 | -0.1031 | 0.2843 | 0.6137 | 0.3377 | 0.1888 | 0.7 | 0.0262 | -0.0207 | 0.2934 | -0.0501 | 0.3704 | -11.6098 | 2.826 | -27.9328 | 33 | 2.9473 | 0.1594 | 3.7551 | 7.9449 | -0.3446 | 4.8641 | -0.1576 | 0.5825 | -0.2618 | -0.5861 | -0.3107 | -0.4219 | -0.3388 | 0.4343 | 0.0772 | 1.0887 | 0.2883 | 0.3253 | 0.8902 | -0.1996 | 0.8759 | -3.8066 | -0.7524 | -38.4496 | 34 | 5.73 | -1.2586 | -3.5412 | 3.0875 | 0.8614 | 4.3568 | 0.0166 | -0.0078 | -1.0165 | -0.438 | -0.2493 | 0.2543 | 0.1836 | -0.0358 | 0.2454 | 0.5191 | -0.0309 | 0.0294 | 0.2496 | 0.0387 | 0.4967 | -12.0664 | -3.4614 | -18.8919 | 35 | 2.0088 | 0.0612 | 2.0448 | 6.6244 | 0.4568 | 5.7302 | -0.3066 | -0.6155 | -0.8576 | 0.9062 | 0.1689 | 1.1004 | 0.8148 | -1.068 | 0.2339 | 0.5069 | -0.0905 | 0.1585 | 0.468 | 0.0987 | 0.5413 | -24.8115 | 3.8682 | 0.2528 | 36 | 1.0645 | -0.3061 | 0.1617 | 3.0308 | 0.3215 | 1.7118 | -0.005 | 0.1648 | 0.0971 | -0.1503 | 0.034 | 0.3818 | -0.0175 | -0.3938 | -0.0155 | 0.2332 | -0.0086 | -0.0137 | 0.2801 | 0.1099 | 0.2609 | -24.7512 | 48.8546 | -27.7266 | 37 | 0.4488 | -0.5526 | -0.2374 | 0.8339 | -0.025 | 0.7238 | 0.1039 | 0.1585 | 0.2027 | -0.3246 | 0.0315 | 0.5058 | -0.1097 | -0.2921 | -0.0206 | 0.3313 | 0.0777 | -0.0808 | 0.3883 | 0.1794 | 0.443 | -30.066 | 54.7589 | -30.2849 | 38 | 0.8744 | -0.9903 | -0.217 | 1.9598 | -0.1949 | 6.4877 | 0.1294 | 0.3019 | 0.0245 | -0.1986 | 0.0988 | -0.6462 | -0.06 | 0.436 | -0.0783 | 0.3558 | -0.064 | 0.1391 | 0.3526 | 0.1482 | 0.5491 | -5.6004 | 54.7625 | -34.3785 | 39 | 1.5403 | -0.3653 | 1.3379 | 2.6285 | -0.2275 | 2.4128 | 0.1609 | 0.2139 | 0.192 | -0.571 | -0.106 | 0.4641 | -0.0794 | -0.0428 | -0.046 | 0.3526 | 0.0665 | -0.0336 | 0.3995 | 0.0603 | 0.3546 | -22.8094 | 45.1549 | -33.8481 | 40 | 2.5114 | 0.3974 | 0.2791 | 0.2786 | -0.229 | 4.1563 | 0.0816 | -0.2907 | -0.0349 | 0.0095 | -0.1162 | -0.0835 | -0.1363 | 0.4713 | 0.2398 | 0.7058 | -0.2096 | 0.4164 | 0.8702 | 0.1698 | 0.9057 | -4.6995 | 62.8724 | -35.7757 | 41 | 4.1842 | 0.407 | -0.854 | 1.8457 | 0.0398 | 2.0824 | 0.3357 | 0.3246 | 0.0318 | -0.8051 | -0.0278 | -0.0276 | -0.031 | -0.1665 | -0.3446 | 0.5954 | 0.1617 | -0.0228 | 0.5397 | 0.1662 | 0.3574 | -22.6295 | 56.0509 | -42.0132 | 42 | 5.6795 | -4.3987 | 2.7587 | 3.863 | -1.3784 | 3.8941 | 0.1173 | -0.4258 | -0.6378 | -0.1908 | 0.3315 | 0.8892 | 0.3275 | -0.8006 | -0.1907 | 0.4574 | 0.0064 | -0.354 | 0.5421 | 0.1598 | 0.6207 | -41.8795 | 41.0894 | -41.1458 |
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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 0:23)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 24:82)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 83:129)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 130:152)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 153:214)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 215:222)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 223:242)8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resseq 243:256)9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 0:23)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 24:82)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 83:100)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 101:129)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 130:152)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 153:214)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 215:222)16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resseq 223:242)17 | X-RAY DIFFRACTION | 17 | chain 'B' and (resseq 243:256)18 | X-RAY DIFFRACTION | 18 | chain 'C' and ( | | | | | | | | | | | | | | | | | |
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