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 / Resolution: 2.99→48.44 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.8 / σ(F): 1.34 / Phase error: 24.43 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.24 | 1942 | 5.02 % |
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Rwork | 0.186 | - | - |
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obs | 0.189 | 38654 | 99.6 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.86 Å2 / ksol: 0.31 e/Å3 |
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Displacement parameters | Biso mean: 59.96 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -5.7223 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 26.4041 Å2 | 0 Å2 |
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3- | - | - | -20.6818 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.99→48.44 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 9457 | 0 | 65 | 36 | 9558 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.003 | 9738 | X-RAY DIFFRACTION | f_angle_d0.847 | 13186 | X-RAY DIFFRACTION | f_dihedral_angle_d13.442 | 3479 | X-RAY DIFFRACTION | f_chiral_restr0.161 | 1671 | X-RAY DIFFRACTION | f_plane_restr0.002 | 1567 | | | | | |
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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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2.9932-3.0681 | 0.362 | 144 | 0.2722 | 2483 | X-RAY DIFFRACTION | 96 | 3.0681-3.151 | 0.2825 | 130 | 0.2277 | 2592 | X-RAY DIFFRACTION | 100 | 3.151-3.2437 | 0.2446 | 121 | 0.2121 | 2600 | X-RAY DIFFRACTION | 100 | 3.2437-3.3484 | 0.3455 | 149 | 0.2218 | 2618 | X-RAY DIFFRACTION | 100 | 3.3484-3.468 | 0.3011 | 143 | 0.211 | 2606 | X-RAY DIFFRACTION | 100 | 3.468-3.6068 | 0.2748 | 130 | 0.1928 | 2618 | X-RAY DIFFRACTION | 100 | 3.6068-3.7709 | 0.2661 | 148 | 0.1728 | 2591 | X-RAY DIFFRACTION | 100 | 3.7709-3.9697 | 0.2221 | 121 | 0.1633 | 2626 | X-RAY DIFFRACTION | 100 | 3.9697-4.2182 | 0.2084 | 127 | 0.1478 | 2656 | X-RAY DIFFRACTION | 100 | 4.2182-4.5437 | 0.1588 | 141 | 0.1321 | 2612 | X-RAY DIFFRACTION | 100 | 4.5437-5.0005 | 0.1796 | 126 | 0.1342 | 2649 | X-RAY DIFFRACTION | 100 | 5.0005-5.7231 | 0.2898 | 164 | 0.1956 | 2634 | X-RAY DIFFRACTION | 100 | 5.7231-7.2067 | 0.2158 | 154 | 0.1993 | 2662 | X-RAY DIFFRACTION | 100 | 7.2067-48.4485 | 0.2247 | 144 | 0.2238 | 2765 | X-RAY DIFFRACTION | 99 |
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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 | 0.7969 | -0.0519 | 0.8054 | 2.8213 | -0.3907 | 2.4021 | -0.1346 | 0.2236 | -0.0859 | -0.0336 | -0.0618 | -0.1601 | -0.3432 | -0.1834 | 0.0377 | 0.3058 | 0.1695 | -0.1203 | 0.3295 | 0.0112 | 0.2767 | -17.5921 | 48.3791 | -40.2958 | 2 | 1.0491 | 0.0702 | -0.2515 | 0.8155 | 0.1205 | 1.0978 | 0.1792 | -0.0227 | 0.0048 | 0.105 | -0.0257 | 0.0986 | -0.0104 | 0.1103 | -0.0481 | 0.1963 | 0.0313 | 0.0635 | 0.4385 | 0.0707 | 0.1767 | -15.605 | 36.8707 | -18.0009 | 3 | 0.8329 | 0.0614 | -0.6224 | 0.2446 | 0.2336 | 0.7875 | 0.0841 | 0.0464 | 0.0939 | -0.0291 | 0.0412 | 0.2321 | -0.2853 | -0.5116 | -0.1729 | 0.1568 | 0.1131 | 0.0229 | 0.5725 | -0.0589 | 0.2419 | -24.7564 | 47.0584 | -27.0337 | 4 | 0.7144 | -0.691 | 0.2392 | 1.3894 | 0.853 | 1.7184 | -0.2466 | -0.388 | -0.0646 | 0.3125 | -0.0983 | -0.0456 | 0.2673 | -0.1336 | 0.1338 | 0.4354 | 0.1316 | 0.1265 | 0.8486 | -0.0368 | 0.3299 | -19.768 | 39.8066 | -3.154 | 5 | 1.0135 | -0.3095 | 0.1958 | 0.8283 | 0.0984 | 0.8668 | -0.0052 | -0.069 | -0.1946 | 0.0361 | 0.0051 | 0.1846 | -0.1682 | -0.442 | -0.0932 | 0.2431 | 0.1239 | -0.0206 | 0.3697 | 0.0228 | 0.1626 | -12.3791 | 45.6772 | -20.3924 | 6 | 0.4417 | -0.0804 | 0.2387 | 0.428 | 0.3648 | 1.9402 | -0.1867 | 0.0651 | -0.0932 | 0.0809 | 0.0148 | 0.2021 | -0.1596 | -0.561 | -0.1357 | 0.644 | -0.0154 | 0.1047 | 0.9588 | -0.1184 | 0.2698 | -27.9953 | 39.7909 | -1.4561 | 7 | 1.1729 | -0.3038 | -0.3331 | 1.197 | 0.2355 | 0.4968 | -0.0356 | -0.2069 | 0.2113 | 0.1058 | -0.0905 | 0.0333 | 0.018 | -0.0321 | -0.2455 | 0.2596 | 0.1917 | -0.0016 | 0.2705 | -0.1601 | 0.2888 | -22.7797 | 53.2503 | -15.924 | 8 | 1.2573 | -0.0029 | 0.449 | 1.0938 | 0.3981 | 0.3062 | 0.1041 | 0.3386 | -0.0876 | -0.3267 | -0.234 | 0.2199 | -0.2713 | -0.1348 | 0.0234 | 0.5178 | 0.2588 | 0.0132 | 0.3854 | -0.0383 | 0.3652 | -10.1966 | 59.2459 | -35.6089 | 9 | 3.2835 | 0.1437 | -0.456 | 1.8884 | -0.0587 | 2.9103 | 0.1899 | 0.1699 | -0.096 | -0.1514 | 0.0829 | -0.0103 | -0.2332 | -0.0121 | -0.0483 | 0.2169 | -0.1621 | -0.0793 | 0.2826 | 0.1066 | 0.1718 | 10.7156 | 54.8421 | -43.1045 | 10 | 1.5421 | -0.2252 | -0.0607 | 1.5391 | 0.3315 | 1.6048 | -0.1453 | -0.2258 | 0.0759 | -0.0677 | 0.0758 | -0.1162 | 0.0004 | 0.02 | 0.0412 | 0.1851 | 0.0288 | 0.0108 | 0.2415 | -0.0733 | 0.1766 | 2.4903 | 50.6631 | -19.7537 | 11 | 0.6689 | -0.2576 | 0.3237 | 1.3452 | 0.4528 | 0.4475 | -0.069 | 0.0099 | 0.072 | -0.1583 | -0.0208 | 0.2192 | -0.3069 | 0.4757 | -0.0318 | 0.3788 | -0.1426 | -0.0284 | 0.5704 | -0.0651 | 0.3628 | 16.1623 | 57.9726 | -37.7573 | 12 | 0.4319 | 0.049 | -0.0323 | 0.9072 | 0.1177 | 0.1722 | 0.0208 | -0.171 | 0.2031 | 0.1745 | -0.0029 | 0.0814 | -0.2247 | 0.037 | -0.0902 | 0.524 | -0.0492 | -0.1236 | 0.1898 | -0.2243 | 0.2979 | 4.2124 | 63.6973 | -25.9337 | 13 | 1.1816 | -0.3801 | -0.0119 | 1.2848 | -1.154 | 1.5851 | -0.1014 | -0.2088 | 0.138 | 0.3599 | -0.2143 | 0.2045 | -0.4108 | 0.2026 | -0.5051 | 0.4841 | 0.0189 | -0.0071 | 0.4629 | -0.2136 | 0.231 | 4.977 | 56.9437 | -5.5419 | 14 | 1.2297 | -0.0133 | -0.4224 | 0.9948 | -0.313 | 1.3583 | -0.0274 | -0.1817 | 0.1669 | 0.0015 | -0.0339 | 0.0898 | -0.2244 | 0.0598 | 0.08 | 0.2194 | -0.0089 | -0.0084 | 0.38 | -0.0189 | 0.2058 | 11.7153 | 50.0748 | -22.7636 | 15 | 0.222 | 0.1555 | 0.3263 | 0.1083 | 0.2285 | 0.4796 | 0.0974 | -0.3126 | 0.2417 | 0.1776 | 0.0603 | 0.138 | -0.5943 | -0.2738 | -0.0052 | 1.1001 | 0.3083 | 0.1549 | 1.105 | -0.2798 | 0.5068 | 2.7757 | 65.0278 | -4.3107 | 16 | 1.3685 | -0.3636 | -0.2113 | 0.8093 | -0.6862 | 0.8077 | -0.1684 | -0.2637 | 0.1545 | 0.2086 | -0.0504 | -0.1635 | -0.2642 | -0.103 | 0.1855 | 0.3295 | -0.1675 | -0.1089 | 0.3668 | -0.104 | 0.299 | 15.935 | 62.6543 | -19.6967 | 17 | 0.929 | -0.8474 | -0.965 | 2.54 | 0.7315 | 1.3306 | -0.0315 | 0.3443 | 0.37 | -0.3127 | -0.0788 | 0.13 | -0.2193 | 0.0832 | 0.0031 | 0.2166 | -0.1688 | -0.0287 | 0.5413 | 0.0706 | 0.3837 | 24.5069 | 50.6377 | -39.4208 | 18 | 0.4489 | 0.3731 | -0.1368 | 1.7415 | 0.5935 | 3.6123 | -0.0308 | 0.0628 | -0.1 | 0.02 | -0.1677 | 0.1511 | 0.1005 | 0.1318 | 0.0695 | 0.3989 | 0.0278 | 0.1048 | 0.1027 | -0.0199 | 0.0449 | 6.4182 | 6.1146 | -42.7252 | 19 | 0.2489 | -0.1229 | 0.0424 | 0.1404 | -0.0619 | 0.0301 | -0.0306 | -0.1056 | -0.045 | -0.0448 | -0.0471 | -0.0783 | 0.2386 | 0.1306 | -0.1843 | 0.3501 | 0.5474 | -0.0841 | 0.096 | 0.2579 | 0.1002 | 14.3306 | 9.7456 | -25.486 | 20 | 0.6204 | -0.2843 | -0.4948 | 0.6938 | -0.315 | 1.2668 | -0.066 | -0.2882 | -0.2044 | 0.443 | -0.0344 | -0.3476 | 0.447 | 0.3659 | 0.042 | 0.8507 | 0.1553 | -0.1723 | 0.7808 | 0.2715 | 0.5136 | 18.7395 | 9.8812 | -6.9626 | 21 | 1.0837 | 0.2559 | -0.165 | 0.0618 | -0.0399 | 0.0266 | -0.006 | 0.1866 | -0.2587 | -0.1955 | 0.2802 | -0.0246 | 0.5164 | -0.1065 | -0.1791 | 0.6613 | 0.0273 | -0.0119 | 0.245 | 0.032 | 0.2949 | 2.5166 | 12.0903 | -24.4718 | 22 | 2.9881 | 1.8009 | -0.7863 | 2.3396 | 0.2142 | 0.5854 | 0.4256 | -1.0254 | -0.5682 | 0.6452 | 0.0498 | -0.302 | 0.6977 | 0.6299 | -0.2451 | 0.8115 | 0.4185 | -0.0291 | 0.8967 | 0.14 | 0.5068 | 19.2486 | 5.7752 | -13.5385 | 23 | 0.3789 | -0.1245 | 0.0965 | 0.7493 | -0.1402 | 0.1758 | -0.0081 | 0.0061 | -0.1108 | -0.1913 | -0.0298 | 0.1244 | 0.2028 | 0.0341 | -0.1703 | 0.9046 | 0.0383 | 0.0499 | 0.1409 | 0.0779 | 0.4221 | 4.8221 | -0.4729 | -24.7119 | 24 | 3.8869 | -0.6155 | 0.9692 | 0.783 | 1.4944 | 4.2023 | 0.7214 | 0.4277 | -0.0126 | -0.9026 | -0.2945 | 0.1396 | -0.1733 | 0.1826 | -0.4699 | 1.309 | 0.1124 | 0.1231 | 0.4285 | -0.1129 | 0.5467 | -10.6114 | 0.622 | -45.3484 | 25 | 3.4419 | -0.4196 | -0.3079 | 0.5679 | -0.1836 | 2.3114 | -0.0292 | -0.0569 | 0.1653 | -0.1652 | -0.1738 | 0.3174 | 0.5691 | -0.4583 | 0.1556 | 0.4395 | -0.1951 | 0.0547 | 0.6377 | -0.0924 | 0.286 | -21.3701 | 17.9729 | -39.9377 | 26 | 0.7896 | -0.1593 | -0.3396 | 1.4158 | -0.1315 | 0.1747 | -0.1586 | 0.0052 | -0.0301 | 0.1658 | 0.16 | 0.0611 | 0.562 | -0.1306 | 0.0114 | 0.5338 | -0.0329 | 0.0353 | 0.3111 | 0.1628 | 0.3275 | -8.2627 | 15.2069 | -18.7503 | 27 | 0.5159 | 0.0622 | -0.9318 | 1.3543 | -0.1772 | 1.6864 | -0.1813 | 0.2083 | -0.294 | 0.0932 | -0.1945 | 0.2563 | 0.6101 | -0.6598 | 0.1717 | 0.5188 | -0.2089 | 0.0643 | 0.5894 | 0.0537 | 0.4304 | -26.5157 | 18.3607 | -33.597 | 28 | 1.0004 | 0.3536 | -0.1977 | 0.9277 | -0.2863 | 0.5228 | -0.0308 | 0.0222 | -0.1802 | 0.0744 | -0.0965 | -0.086 | 0.3967 | -0.0734 | -0.5171 | 0.5735 | -0.2413 | 0.1696 | 0.2724 | 0.1114 | 0.3101 | -18.3189 | 6.0795 | -23.8329 | 29 | 1.1173 | 0.2661 | 0.4577 | 0.965 | 0.6086 | 0.814 | -0.2675 | -0.5027 | -0.3138 | 0.1566 | 0.0072 | -0.1139 | 0.6633 | 0.0052 | 0.0447 | 0.8666 | -0.0335 | 0.0063 | 0.6002 | 0.274 | 0.4308 | -11.4224 | 10.865 | -3.9765 | 30 | 0.9575 | -0.143 | 0.4026 | 1.3891 | 0.2298 | 0.2379 | -0.136 | -0.2397 | -0.2103 | -0.0447 | 0.3355 | 0.1777 | 0.3944 | -0.5361 | -0.168 | 0.3926 | -0.0788 | 0.0601 | 0.4556 | 0.0876 | 0.3752 | -21.6707 | 23.3242 | -20.4936 | 31 | 1.5844 | -0.4891 | 1.0909 | 2.0613 | -0.0807 | 1.1445 | 0.3058 | 0.1183 | -0.0845 | -0.2367 | 0.0043 | -0.0936 | 0.3214 | -0.2573 | -0.1548 | 0.2682 | 0.0408 | -0.0177 | 0.3038 | -0.0825 | 0.2519 | -9.3814 | 27.0962 | -24.8918 | 32 | 1.2332 | -0.4712 | 0.1966 | 0.8831 | 0.0382 | 0.0508 | -0.1815 | -0.3132 | -0.5998 | 0.5088 | 0.3443 | 0.0399 | 0.6607 | -0.4547 | -0.234 | 0.7911 | -0.1618 | 0.0507 | 0.4465 | 0.1608 | 0.4465 | -16.0312 | 10.9251 | -13.2423 | 33 | 0.3226 | 0.1137 | -0.0701 | 0.1004 | 0.1005 | 0.2751 | 0.0015 | -0.1204 | -0.1192 | -0.0967 | -0.2291 | -0.378 | 0.1928 | -0.0752 | 0.254 | 1.6543 | -0.0819 | -0.1043 | 1.071 | 0.4841 | 0.7862 | -14.693 | 3.2483 | -2.6046 | 34 | 1.8885 | -0.2148 | -0.4772 | 1.0051 | 0.167 | 1.1421 | -0.171 | 0.1402 | -0.2025 | 0.3271 | -0.1201 | 0.12 | 0.3679 | -0.1503 | 0.0367 | 0.4898 | -0.2443 | 0.1142 | 0.5762 | 0.0957 | 0.3943 | -26.2423 | 14.1025 | -16.1203 | 35 | 1.273 | 0.3636 | -0.3313 | 0.9333 | 0.1937 | 0.2331 | -0.0015 | -0.1203 | 0.0093 | 0.0595 | -0.1724 | 0.1355 | 0.0386 | 0.0282 | 0.0812 | 0.2053 | -0.1165 | -0.0153 | 0.5984 | 0.0761 | 0.295 | -29.0233 | 29.5763 | -34.8121 | 36 | 0.7149 | 0.1084 | -0.128 | 0.2184 | 0.0846 | 0.8659 | -0.0724 | 0.0792 | -0.0337 | -0.0724 | -0.0206 | -0.1277 | 0.0687 | 0.3883 | -0.0422 | -0.0157 | 0.1574 | 0.0156 | 0.4282 | -0.0016 | 0.0846 | 23.0451 | 34.6541 | -27.815 | 37 | 0.6972 | 0.072 | 0.2859 | 0.31 | -0.1918 | 0.275 | -0.0116 | 0.1048 | 0.0162 | -0.0339 | -0.0519 | -0.2448 | 0.043 | 0.4553 | -0.1952 | -0.0585 | 0.0943 | -0.1019 | 0.5791 | -0.0702 | 0.2197 | 30.0425 | 34.6374 | -32.46 | 38 | 0.4158 | 0.1437 | 0.0536 | 0.3476 | -0.8062 | 2.2764 | -0.1869 | -0.2049 | 0.1749 | 0.2124 | -0.1724 | -0.2052 | -0.0711 | 0.6736 | 0.101 | 0.3467 | 0.1006 | -0.1169 | 0.9159 | -0.1105 | 0.3534 | 28.86 | 38.4755 | -7.9774 | 39 | 0.7567 | -0.0632 | -0.0777 | 0.9627 | 0.0154 | 0.1674 | 0.0122 | 0.1915 | 0.0929 | 0.0925 | 0.0199 | -0.1551 | 0.1439 | 0.8374 | 0.013 | 0.2705 | 0.1756 | -0.0116 | 0.5997 | 0.0702 | 0.2411 | 23.2967 | 28.3447 | -23.9427 | 40 | 1.1748 | -0.8076 | 1.4785 | 1.0331 | -0.5252 | 2.3654 | -0.073 | -0.0562 | -0.0018 | 0.0941 | 0.2436 | -0.1927 | 0.1931 | 0.5044 | -0.1983 | 0.4827 | -0.0348 | -0.1408 | 1.3162 | -0.1119 | 0.4259 | 35.9828 | 42.0288 | -6.8626 | 41 | 2.6025 | -0.1207 | -1.0743 | 1.0174 | 0.0275 | 0.7394 | -0.0667 | -0.6691 | -0.198 | 0.2063 | -0.1031 | -0.1081 | 0.0839 | 0.358 | 0.1712 | 0.1207 | 0.1756 | 0.019 | 0.6267 | 0.0967 | 0.3711 | 36.7465 | 28.4507 | -21.7279 | 42 | 2.531 | -1.4068 | -0.1124 | 2.3202 | -0.1654 | 0.301 | 0.0307 | -0.0624 | -0.1038 | -0.0325 | 0.0802 | 0.2248 | 0.0408 | 0.0545 | 0.2988 | 0.5331 | 0.4023 | -0.0436 | 0.5388 | -0.0053 | 0.5399 | 26.8099 | 15.0058 | -39.6432 |
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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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