ソフトウェア | 名称 | バージョン | 分類 | NB |
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d*TREK | 8.0SSIデータスケーリング | | REFMAC | 5.2.0005精密化 | | PDB_EXTRACT | 2 | データ抽出 | | CrystalClear | | データ収集 | | CrystalClear | | データ削減 | | PHASER | | 位相決定 | | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: pdb entry 1GD7 解像度: 1.55→52.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.894 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.208 | 1727 | 5.1 % | RANDOM |
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Rwork | 0.178 | - | - | - |
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obs | 0.18 | 34099 | 99.7 % | - |
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all | - | 34099 | - | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 7.929 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.21 Å2 | -0.11 Å2 | 0 Å2 |
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2- | - | -0.21 Å2 | 0 Å2 |
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3- | - | - | 0.32 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.55→52.53 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1677 | 0 | 25 | 350 | 2052 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.01 | 0.022 | 1731 | X-RAY DIFFRACTION | r_angle_refined_deg1.282 | 1.993 | 2341 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.318 | 5 | 218 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.975 | 24.118 | 68 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg10.815 | 15 | 281 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.079 | 15 | 11 | X-RAY DIFFRACTION | r_chiral_restr0.093 | 0.2 | 267 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 1295 | X-RAY DIFFRACTION | r_nbd_refined0.193 | 0.2 | 745 | X-RAY DIFFRACTION | r_nbtor_refined0.312 | 0.2 | 1206 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.111 | 0.2 | 258 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.186 | 0.2 | 36 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.118 | 0.2 | 27 | X-RAY DIFFRACTION | r_mcbond_it0.546 | 1.5 | 1128 | X-RAY DIFFRACTION | r_mcangle_it0.828 | 2 | 1800 | X-RAY DIFFRACTION | r_scbond_it1.473 | 3 | 654 | X-RAY DIFFRACTION | r_scangle_it2.218 | 4.5 | 541 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.55→1.59 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.613 | 126 | - |
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Rwork | 0.508 | 2389 | - |
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obs | - | 2515 | 99.56 % |
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精密化 TLS | 手法: 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 | 7.4738 | 6.3385 | -6.3263 | 17.1546 | -9 | 10.8174 | -0.0728 | 0.1546 | -0.0877 | -0.6764 | 0.0143 | 0.0016 | 0.4213 | -0.1535 | 0.0585 | 0.0638 | 0.0077 | -0.0053 | 0.0545 | -0.0159 | -0.0396 | -37.708 | -7.385 | 10.37 | 2 | 11.7907 | 1.9314 | -3.928 | 2.5792 | 1.3726 | 7.5105 | 0.1033 | -0.1248 | 0.5182 | -0.013 | 0.041 | 0.0055 | -0.16 | 0.3571 | -0.1443 | 0.0484 | 0.022 | 0.0157 | 0.0222 | -0.0017 | -0.0257 | -31.576 | -2.715 | 8.368 | 3 | 0.2373 | -0.566 | 1.0129 | 1.3883 | -1.606 | 21.5876 | -0.1822 | -0.1375 | 0.0378 | 0.0037 | -0.102 | 0.061 | -0.3451 | -0.3546 | 0.2842 | 0.0333 | 0.0028 | 0.002 | 0.0711 | -0.0149 | -0.0145 | -26.191 | -2.754 | -0.796 | 4 | 6.3061 | -4.7119 | -2.6839 | 9.2579 | 3.8875 | 2.8306 | -0.0461 | -0.1089 | 0.0594 | 0.1069 | 0.1141 | -0.3389 | 0.025 | 0.1144 | -0.068 | 0.0516 | 0.0076 | 0.0113 | 0.0265 | 0.0107 | -0.0289 | -17.079 | -7.1 | -13.573 | 5 | 4.7545 | -3.1924 | 1.5686 | 9.6178 | -4.102 | 12.109 | 0.0127 | -0.1942 | 0.0932 | -0.0881 | -0.2496 | -0.4062 | 0.4365 | 0.677 | 0.2369 | 0.0261 | 0.0138 | 0.0016 | 0.0283 | 0.0059 | -0.0327 | -10.887 | -20.696 | -9.869 | 6 | 13.0995 | -6.5173 | 6.8659 | 13.6765 | -5.5115 | 9.4785 | 0.3297 | -0.6468 | -0.7067 | 0.5669 | 0.2395 | 0.9572 | 0.2858 | -0.0274 | -0.5692 | 0.0936 | -0.0001 | -0.0042 | 0.033 | 0.0199 | 0.0074 | -16.555 | -24.659 | -7.347 | 7 | 0.7535 | -3.3599 | -0.5935 | 20.3817 | 0.793 | 4.0701 | 0.0224 | -0.0515 | 0.0823 | 0.1946 | -0.0367 | -0.6556 | 0.0808 | 0.1001 | 0.0143 | 0.0391 | 0.0029 | -0.0011 | 0.0264 | 0.0082 | -0.0055 | -15.265 | -8.256 | -9.73 | 8 | 10.8351 | 9.7717 | 8.364 | 23.6062 | 2.337 | 8.4951 | -0.3725 | -0.4432 | 0.6839 | 0.1922 | -0.1814 | 0.5437 | -0.516 | 0.1338 | 0.5539 | 0.0555 | 0.0033 | -0.0026 | 0.0186 | -0.0214 | -0.0043 | -18.599 | 2.443 | -5.239 | 9 | 2.1594 | 2.5876 | 0.7189 | 16.9512 | 1.6597 | 0.8498 | 0.1698 | -0.0799 | 0.0103 | 0.0993 | -0.4136 | -0.3947 | 0.0441 | -0.0104 | 0.2438 | 0.0495 | 0.0084 | 0.0037 | 0.0282 | 0.0123 | -0.0197 | -15.215 | -9.048 | -5.704 | 10 | 1.9543 | 1.5569 | -2.1266 | 4.982 | -0.2064 | 2.9165 | 0.0592 | 0.1182 | -0.1436 | 0.1019 | -0.0206 | -0.1019 | 0.0258 | -0.0412 | -0.0386 | 0.028 | 0.0011 | 0.0156 | 0.0153 | -0.0069 | -0.0263 | -23.088 | -20.125 | -13.68 | 11 | 2.3232 | -3.7226 | -2.4485 | 14.7366 | 3.263 | 2.6303 | 0.3173 | 0.2711 | -0.1301 | -0.3794 | -0.3645 | 0.1583 | -0.1796 | 0.0697 | 0.0473 | 0.0453 | 0.0194 | -0.016 | 0.0649 | 0.0082 | -0.0336 | -18.798 | -12.497 | -18.696 | 12 | 0.6142 | 0.4962 | 0.0031 | 1.8094 | -1.8038 | 6.3231 | -0.0877 | -0.0118 | 0.1191 | -0.1163 | 0.0942 | -0.0125 | 0.1761 | -0.2067 | -0.0065 | 0.0403 | -0.0015 | 0.0055 | 0.0289 | 0.0015 | -0.0232 | -25.357 | -7.315 | -9.087 | 13 | 4.5677 | -2.9446 | -0.6357 | 2.9834 | 1.0262 | 2.4641 | -0.1036 | -0.3131 | -0.0539 | 0.1853 | 0.1097 | -0.0375 | 0.1793 | 0.0037 | -0.0061 | 0.0238 | -0.0003 | -0.0032 | 0.0682 | -0.0138 | -0.0416 | -18.095 | -9.092 | 4.06 | 14 | 4.4469 | -0.6078 | -0.2147 | 2.3232 | -2.6172 | 3.1371 | 0.0139 | 0.0505 | -0.0077 | -0.1607 | -0.0361 | 0.0378 | 0.0434 | 0.0225 | 0.0222 | 0.0409 | 0.0109 | -0.0166 | 0.0333 | 0.0054 | -0.0301 | -10.32 | -15.447 | -0.371 | 15 | 14.6022 | 1.8898 | 1.8034 | 0.2863 | 0.4727 | 1.5941 | -0.1193 | -0.1421 | 0.1334 | -0.0283 | 0.0124 | 0.0627 | -0.0638 | 0.0303 | 0.1069 | 0.0365 | 0.0014 | 0.0017 | 0.0196 | 0.0021 | -0.0227 | -21.594 | -10.847 | -2.762 | 16 | 4.9274 | -2.5422 | -0.2495 | 8.3028 | 3.5985 | 5.0881 | -0.1322 | 0.1575 | -0.4934 | 0.1304 | -0.0537 | 0.2016 | 0.2858 | -0.0235 | 0.1859 | 0.028 | -0.027 | 0.041 | 0.0121 | -0.0103 | 0.0163 | -32.504 | -22.735 | -8.428 | 17 | 1.6605 | -1.6546 | 0.2984 | 16.1093 | 0.7134 | 0.5555 | 0.0463 | 0.0552 | -0.1901 | 0.1717 | -0.0654 | 0.0737 | 0.0031 | -0.0765 | 0.0191 | 0.0263 | -0.0065 | 0.0144 | 0.0333 | -0.0132 | -0.0168 | -28.753 | -16.816 | -10.051 | 18 | 8.3408 | 4.9629 | 3.4936 | 4.2392 | 2.0429 | 4.3088 | -0.0746 | -0.0557 | 0.2263 | -0.0874 | 0.1298 | -0.0056 | -0.0241 | -0.2186 | -0.0552 | 0.0147 | 0.0153 | -0.0031 | 0.0464 | 0.0075 | -0.0291 | -32.018 | -0.781 | -14.188 | 19 | 13.1153 | 1.2904 | -7.3087 | 1.4549 | -0.6207 | 4.081 | 0.1437 | -0.1522 | 0.2983 | -0.002 | -0.0282 | 0.1942 | -0.1849 | -0.0513 | -0.1156 | 0.0119 | 0.0006 | 0.0035 | 0.0319 | -0.0039 | -0.0333 | -28.752 | 0.74 | -4.224 | 20 | 11.9852 | 7.4513 | -2.1223 | 37.2751 | -7.1862 | 7.0632 | -0.4339 | -0.2077 | -0.1965 | -0.7395 | 0.5323 | -0.2682 | 0.0833 | 0.1861 | -0.0984 | 0.0057 | 0.0558 | -0.004 | 0.1439 | -0.0664 | -0.1093 | -22.131 | -7.33 | 8.358 | 21 | 21.2075 | 7.0294 | 3.8772 | 3.2269 | 4.9387 | 15.5923 | -0.296 | -0.1662 | -0.505 | 0.1235 | 0.3159 | 0.0778 | 0.3261 | 0.4149 | -0.0199 | 0.0714 | 0.0633 | 0.0059 | 0.0257 | 0.0193 | -0.0469 | -28.422 | -12.032 | 9.017 | 22 | 1.9667 | 1.0911 | 3.3042 | 4.0679 | 4.4836 | 7.6423 | 0.1039 | 0.0303 | -0.0016 | 0.0973 | -0.0562 | 0.0039 | 0.2351 | 0.1289 | -0.0477 | 0.0515 | -0.0068 | 0.0034 | 0.0647 | -0.0049 | -0.0269 | -36.549 | -13.376 | 1.313 | 23 | 5.5174 | -2.6871 | 1.7237 | 1.7751 | -1.2786 | 2.3686 | 0.1665 | 0.0007 | 0.1189 | -0.0515 | -0.2122 | -0.0047 | -0.0321 | -0.0124 | 0.0457 | 0.0138 | -0.0063 | -0.0218 | 0.015 | -0.0101 | -0.0125 | -48.879 | -10.381 | -8.996 | 24 | 15.7504 | -7.6399 | -2.2647 | 4.0273 | 0.1412 | 3.1762 | -0.0703 | -0.7899 | 1.8472 | -0.0769 | -0.0411 | 0.5382 | -0.2232 | -0.2281 | 0.1114 | 0.0073 | 0.0302 | -0.0548 | -0.0158 | -0.0888 | 0.2204 | -52.713 | 4.016 | -6.212 | 25 | 3.263 | -2.021 | 1.0182 | 10.159 | -1.1061 | 0.8932 | -0.0343 | -0.1128 | 0.207 | -0.0132 | -0.0059 | 0.221 | -0.0508 | -0.0736 | 0.0402 | 0.0248 | -0.0068 | 0.0102 | 0.0279 | -0.0304 | -0.0141 | -48.448 | -7.65 | -4.99 | 26 | 7.1116 | 0.0946 | 1.4167 | 11.7636 | -1.0571 | 9.5386 | -0.0186 | -0.4686 | -0.1599 | 0.1505 | 0.0825 | -0.2772 | 0.2971 | 0.0465 | -0.0639 | 0.0266 | -0.0168 | 0.0152 | 0.0453 | -0.0094 | -0.0102 | -46.556 | -19.301 | 0.141 | 27 | 2.2878 | 4.5971 | -4.0079 | 16.6233 | -6.5725 | 7.318 | 0.3401 | -0.1952 | 0.2837 | 0.6372 | -0.3425 | 0.2418 | -0.3135 | 0.1874 | 0.0023 | 0.0077 | -0.0106 | 0.0012 | 0.0525 | -0.0261 | 0.035 | -47.166 | -3.578 | -1.781 | 28 | 9.6407 | 2.8896 | -1.7469 | 3.3408 | -1.7372 | 0.9117 | 0.1289 | 0.4029 | 0.7131 | 0.035 | 0.1703 | 0.3203 | 0.0907 | 0.0985 | -0.2992 | -0.0136 | 0.0314 | -0.0041 | 0.0445 | 0.0751 | 0.034 | -43.251 | 2.056 | -13.399 | 29 | 2.4734 | 5.206 | -0.0352 | 24.6383 | -4.0768 | 1.1716 | 0.1388 | 0.5332 | 0.2891 | -0.5304 | 0.0054 | 0.7846 | 0.213 | -0.0194 | -0.1442 | 0.0117 | 0.0245 | -0.0331 | 0.0886 | 0.0282 | -0.0286 | -48.28 | -5.578 | -15.072 | 30 | 1.5065 | 0.8203 | -1.0442 | 2.7871 | 2.9352 | 5.9689 | -0.1078 | 0.0172 | 0.0337 | -0.1549 | 0.0226 | 0.0125 | -0.1084 | 0.0651 | 0.0851 | 0.0329 | 0.0145 | -0.0027 | 0.0185 | 0.0061 | -0.0236 | -39.738 | -9.849 | -7.027 | 31 | 7.6351 | -5.8191 | -1.729 | 4.806 | 1.6857 | 0.7902 | -0.2263 | 0.0067 | 0.1397 | 0.4207 | -0.0008 | 0.2081 | 0.0924 | 0.0546 | 0.227 | 0.0395 | -0.0054 | 0.0156 | 0.0211 | -0.0237 | -0.0088 | -44.853 | -5.972 | 8.087 | 32 | 10.2874 | -9.476 | 0.0026 | 28.1053 | 6.8315 | 6.8433 | -0.0342 | -0.1214 | -0.1025 | 0.1815 | -0.5291 | 0.4799 | 0.1084 | -0.3277 | 0.5633 | 0.0027 | -0.0325 | 0.0278 | 0.0534 | -0.0533 | 0.0165 | -53.232 | -1.936 | 3.94 | 33 | 10.9954 | 2.2436 | -3.8013 | 1.3957 | 0.444 | 2.9003 | 0.0753 | -0.1578 | 0.0014 | 0.06 | -0.1352 | 0.0146 | 0.0452 | 0.0668 | 0.0599 | 0.0272 | -0.0141 | -0.0013 | 0.0212 | -0.004 | -0.0113 | -41.743 | -5.493 | -0.369 | 34 | 14.7709 | -11.0226 | 4.2636 | 13.7496 | -6.9524 | 10.6648 | 0.1318 | 0.3993 | 1.3138 | -0.0259 | -0.3003 | -0.3243 | -0.1779 | 0.2215 | 0.1684 | -0.009 | -0.0054 | 0.0165 | 0.0028 | 0.0621 | 0.0626 | -32.907 | 5.467 | -9.879 | 35 | 2.3269 | -0.1789 | 0.0381 | 9.5763 | -1.526 | 0.5742 | 0.111 | 0.0828 | 0.2831 | 0.0657 | -0.1274 | 0.4179 | 0.0045 | 0.0587 | 0.0164 | 0.0295 | 0.0103 | 0.0173 | 0.0385 | 0.0209 | 0.0003 | -36.876 | -0.557 | -9.828 | 36 | 7.8346 | 1.4726 | -3.059 | 6.233 | -2.5472 | 1.8474 | -0.0091 | -0.0813 | -0.0648 | -0.0533 | -0.024 | 0.1534 | 0.0111 | 0.0765 | 0.0331 | 0.0336 | -0.0095 | 0.007 | 0.0708 | -0.0163 | -0.0478 | -34.601 | -17.056 | -12.832 | 37 | 21.5418 | 2.5819 | 2.3955 | 1.8379 | 0.4698 | 1.6598 | 0.067 | -0.1047 | 0.1509 | -0.0093 | -0.0964 | -0.0716 | 0.1359 | 0.1569 | 0.0294 | 0.0313 | -0.011 | 0.0165 | 0.0338 | -0.0049 | -0.0375 | -35.189 | -17.617 | -2.273 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA2 - 7 | 5 - 10 | 2 | X-RAY DIFFRACTION | 2 | AA8 - 12 | 11 - 15 | 3 | X-RAY DIFFRACTION | 3 | AA13 - 17 | 16 - 20 | 4 | X-RAY DIFFRACTION | 4 | AA18 - 23 | 21 - 26 | 5 | X-RAY DIFFRACTION | 5 | AA24 - 29 | 27 - 32 | 6 | X-RAY DIFFRACTION | 6 | AA30 - 34 | 33 - 37 | 7 | X-RAY DIFFRACTION | 7 | AA35 - 39 | 38 - 42 | 8 | X-RAY DIFFRACTION | 8 | AA40 - 45 | 43 - 48 | 9 | X-RAY DIFFRACTION | 9 | AA46 - 51 | 49 - 54 | 10 | X-RAY DIFFRACTION | 10 | AA52 - 58 | 55 - 61 | 11 | X-RAY DIFFRACTION | 11 | AA59 - 64 | 62 - 67 | 12 | X-RAY DIFFRACTION | 12 | AA65 - 70 | 68 - 73 | 13 | X-RAY DIFFRACTION | 13 | AA71 - 76 | 74 - 79 | 14 | X-RAY DIFFRACTION | 14 | AA77 - 83 | 80 - 86 | 15 | X-RAY DIFFRACTION | 15 | AA84 - 89 | 87 - 92 | 16 | X-RAY DIFFRACTION | 16 | AA90 - 95 | 93 - 98 | 17 | X-RAY DIFFRACTION | 17 | AA96 - 101 | 99 - 104 | 18 | X-RAY DIFFRACTION | 18 | AA102 - 107 | 105 - 110 | 19 | X-RAY DIFFRACTION | 19 | AA108 - 113 | 111 - 116 | 20 | X-RAY DIFFRACTION | 20 | BB2 - 7 | 5 - 10 | 21 | X-RAY DIFFRACTION | 21 | BB8 - 12 | 11 - 15 | 22 | X-RAY DIFFRACTION | 22 | BB13 - 17 | 16 - 20 | 23 | X-RAY DIFFRACTION | 23 | BB18 - 23 | 21 - 26 | 24 | X-RAY DIFFRACTION | 24 | BB24 - 32 | 27 - 35 | 25 | X-RAY DIFFRACTION | 25 | BB33 - 40 | 36 - 43 | 26 | X-RAY DIFFRACTION | 26 | BB41 - 46 | 44 - 49 | 27 | X-RAY DIFFRACTION | 27 | BB47 - 52 | 50 - 55 | 28 | X-RAY DIFFRACTION | 28 | BB53 - 58 | 56 - 61 | 29 | X-RAY DIFFRACTION | 29 | BB59 - 64 | 62 - 67 | 30 | X-RAY DIFFRACTION | 30 | BB65 - 70 | 68 - 73 | 31 | X-RAY DIFFRACTION | 31 | BB71 - 77 | 74 - 80 | 32 | X-RAY DIFFRACTION | 32 | BB78 - 83 | 81 - 86 | 33 | X-RAY DIFFRACTION | 33 | BB84 - 89 | 87 - 92 | 34 | X-RAY DIFFRACTION | 34 | BB90 - 95 | 93 - 98 | 35 | X-RAY DIFFRACTION | 35 | BB96 - 101 | 99 - 104 | |
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