ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | HKL-3000 | | 位相決定 | REFMAC | 5.5.0102精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.55→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.597 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 2 / ESU R: 0.067 / ESU R Free: 0.067 / 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 | 0.169 | 4956 | 5 % | RANDOM |
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Rwork | 0.144 | - | - | - |
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obs | 0.145 | 94110 | 99.5 % | - |
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all | - | 99100 | - | - |
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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: 8.85 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.32 Å2 | 0 Å2 | -1.05 Å2 |
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2- | - | -0.08 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→40 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5109 | 0 | 23 | 880 | 6012 |
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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_d0.016 | 0.022 | 5264 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 3560 | X-RAY DIFFRACTION | r_angle_refined_deg1.509 | 1.963 | 7153 | X-RAY DIFFRACTION | r_angle_other_deg0.935 | 3 | 8687 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.078 | 5 | 652 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg38.193 | 24.286 | 245 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.469 | 15 | 880 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.853 | 15 | 30 | X-RAY DIFFRACTION | r_chiral_restr0.093 | 0.2 | 791 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.021 | 5851 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1071 | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.774 | 1.5 | 3229 | X-RAY DIFFRACTION | r_mcbond_other0.247 | 1.5 | 1307 | X-RAY DIFFRACTION | r_mcangle_it1.39 | 2 | 5223 | X-RAY DIFFRACTION | r_scbond_it2.368 | 3 | 2035 | X-RAY DIFFRACTION | r_scangle_it3.666 | 4.5 | 1925 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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 | 0.293 | 350 | - |
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Rwork | 0.283 | 6787 | - |
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obs | - | - | 97.73 % |
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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 | 0.205 | 0.2587 | -0.1009 | 1.7003 | -0.7473 | 4.2172 | 0.0227 | 0.1058 | -0.0586 | -0.0013 | -0.0981 | 0.0913 | -0.0002 | -0.1863 | 0.0754 | 0.0596 | 0.0118 | -0.0098 | 0.1157 | -0.0298 | 0.0913 | 17.09 | 62.2819 | -3.2916 | 2 | 0.5004 | 0.149 | -0.9142 | 1.9873 | -0.5642 | 5.6258 | 0.0038 | 0.1894 | -0.19 | -0.0691 | -0.0896 | 0.2254 | 0.1164 | -0.4835 | 0.0858 | 0.0527 | -0.0221 | -0.0357 | 0.1675 | -0.0805 | 0.1207 | 12.0229 | 56.5844 | -7.0006 | 3 | 0.9386 | -0.3545 | 0.4203 | 0.5372 | -0.1086 | 1.7284 | 0.0802 | 0.1238 | -0.1328 | -0.0627 | -0.0423 | 0.0295 | 0.0797 | -0.0575 | -0.0379 | 0.0908 | 0.0012 | -0.0071 | 0.1081 | -0.0286 | 0.088 | 23.651 | 59.3094 | -6.2526 | 4 | 6.3053 | 1.9434 | 2.0431 | 2.3962 | 1.785 | 3.2769 | -0.0041 | 0.0859 | -0.241 | 0.0899 | -0.1 | 0.0597 | 0.2478 | -0.0713 | 0.1041 | 0.1033 | -0.0235 | -0.0094 | 0.0873 | -0.0644 | 0.0965 | 21.1101 | 50.9092 | -3.7953 | 5 | 0.8361 | -0.0857 | 0.9902 | 0.1951 | 0.09 | 1.3545 | 0.037 | 0.1988 | -0.0377 | -0.0171 | -0.0062 | 0.0038 | -0.0238 | 0.2117 | -0.0307 | 0.0799 | 0.0014 | 0.0093 | 0.1215 | -0.0188 | 0.067 | 39.6844 | 61.2441 | 2.4251 | 6 | 1.8726 | -0.0592 | -0.044 | 1.0384 | 0.3817 | 0.4708 | 0.0468 | 0.0451 | -0.1126 | 0.1302 | 0.0324 | -0.0409 | 0.1019 | 0.0506 | -0.0792 | 0.113 | 0 | -0.0069 | 0.0661 | -0.0063 | 0.0873 | 44.425 | 57.9878 | 24.6578 | 7 | 6.4012 | -1.2466 | -3.7584 | 2.0442 | 1.5059 | 8.1434 | -0.2547 | -0.0597 | -0.5239 | 0.1694 | 0.0369 | 0.0823 | 0.3165 | 0.3607 | 0.2178 | 0.0917 | 0.0036 | 0.0072 | 0.0349 | -0.0046 | 0.1482 | 39.428 | 48.1969 | 20.1256 | 8 | 3.6149 | 2.587 | 0.331 | 2.9288 | 0.317 | 0.6996 | 0.0124 | 0.2491 | -0.1886 | 0.0224 | 0.1063 | -0.1616 | 0.0367 | 0.1715 | -0.1186 | 0.063 | -0.0027 | -0.0021 | 0.1152 | -0.0415 | 0.0832 | 51.2425 | 57.2768 | 12.751 | 9 | 0.4484 | -0.0705 | 0.2736 | 0.3863 | -0.0737 | 0.6786 | -0.0193 | 0.0788 | 0.0013 | 0.0217 | 0.0154 | 0.0153 | -0.0179 | 0.0386 | 0.0039 | 0.0837 | -0.0174 | 0.0043 | 0.0722 | -0.0027 | 0.0846 | 40.4841 | 66.3823 | 15.3683 | 10 | 2.9313 | -1.3409 | 0.5967 | 3.7223 | 2.36 | 1.7878 | -0.1054 | 0.1741 | 0.2124 | -0.0846 | 0.0858 | -0.1637 | -0.1401 | 0.1246 | 0.0197 | 0.0672 | -0.0317 | -0.0134 | 0.0715 | -0.0013 | 0.0755 | 52.4563 | 73.0448 | 19.0333 | 11 | 1.562 | 0.9129 | 1.1582 | 1.8169 | 0.8115 | 1.6752 | -0.0257 | 0.1995 | 0.14 | -0.0219 | -0.0493 | -0.042 | -0.0516 | 0.1258 | 0.075 | 0.093 | -0.0259 | -0.0106 | 0.078 | 0.0306 | 0.0777 | 41.5485 | 75.2739 | 11.1327 | 12 | 1.1718 | 0.2791 | 0.2571 | 0.2728 | 0.0782 | 0.5865 | -0.0622 | 0.0667 | 0.0663 | -0.0127 | 0.018 | 0.0103 | -0.0639 | -0.0073 | 0.0442 | 0.1006 | -0.0127 | 0 | 0.0539 | 0.0093 | 0.0856 | 29.5943 | 72.2566 | 14.952 | 13 | 0.4102 | -0.3112 | 0.1245 | 1.9197 | 1.1869 | 2.1271 | 0.0658 | 0.1523 | 0.0441 | -0.1402 | -0.1096 | -0.049 | -0.1726 | 0.1072 | 0.0438 | 0.084 | 0.0128 | 0.0062 | 0.1058 | 0.0132 | 0.0616 | 28.685 | 70.7929 | -7.9418 | 14 | 1.8823 | -2.438 | -0.1397 | 14.9631 | 3.4714 | 3.0824 | 0.0806 | 0.3542 | 0.0525 | -0.8327 | 0.0364 | 0.0322 | 0.0645 | 0.4037 | -0.117 | 0.16 | 0.0482 | -0.0037 | 0.1813 | -0.0029 | 0.0126 | 25.4308 | 67.9025 | -19.6972 | 15 | 0.4796 | 0.1876 | -0.4937 | 0.6817 | -0.4334 | 1.684 | 0.0603 | 0.0768 | 0.0394 | -0.0545 | -0.0373 | 0.091 | -0.117 | -0.1279 | -0.023 | 0.0902 | 0.0309 | 0.0022 | 0.1026 | 0.0065 | 0.0756 | 17.3155 | 73.1806 | -4.016 | 16 | 4.074 | 0.6434 | -5.1167 | 4.4362 | -3.3227 | 19.2965 | 0.3745 | -0.1612 | 0.41 | 0.3958 | -0.0029 | 0.1091 | -1.538 | 0.03 | -0.3716 | 0.177 | 0.0683 | 0.0287 | 0.0849 | -0.0273 | 0.1667 | 10.964 | 78.19 | 5.1868 | 17 | 0.839 | 0.4655 | 1.3345 | -0.4458 | 0.7065 | 3.336 | 0.0966 | 0.1639 | -0.0217 | 0.0521 | -0.1116 | 0.1518 | 0.0425 | -0.5286 | 0.015 | 0.0476 | 0.0347 | -0.0216 | 0.3017 | -0.0563 | 0.2269 | 6.7424 | 66.2863 | -4.321 | 18 | 17.3324 | 5.4383 | 24.5128 | 28.3752 | -1.3798 | 30.9102 | -0.8397 | 0.5109 | 1.0542 | -1.0461 | -0.0315 | 0.9073 | -0.6586 | 0.5609 | 0.8712 | 0.0773 | 0.008 | -0.0922 | 0.3613 | 0.1543 | 0.2469 | 7.0629 | 70.4973 | -13.5575 | 19 | 0.8166 | -0.4023 | 0.1774 | 1.6717 | 1.3736 | 4.142 | -0.0544 | -0.158 | -0.0066 | -0.0099 | 0.0245 | 0.0076 | 0.0755 | 0.0401 | 0.0299 | 0.0798 | 0.0273 | 0.0009 | 0.0949 | 0.0002 | 0.0809 | 46.5291 | 66.136 | 46.6683 | 20 | 1.83 | -0.3748 | 0.5901 | 0.3226 | -0.1677 | 1.327 | -0.0334 | -0.2835 | -0.118 | 0.015 | 0.0674 | 0.0286 | 0.0529 | 0.0162 | -0.0339 | 0.0799 | 0.0326 | 0.0095 | 0.1188 | 0.017 | 0.0697 | 48.1357 | 64.4475 | 53.405 | 21 | 3.0165 | -0.3742 | 1.2721 | 0.7661 | -0.518 | 1.1079 | 0.0075 | -0.117 | -0.3337 | 0.018 | 0.0233 | -0.0032 | 0.1975 | -0.0121 | -0.0309 | 0.1174 | 0.0309 | 0.0158 | 0.0771 | 0.0466 | 0.1179 | 41.015 | 55.4617 | 47.9459 | 22 | 0.8031 | 0.1122 | 0.5414 | 0.2511 | 0.0441 | 0.5635 | -0.0392 | -0.1779 | -0.068 | 0.0436 | 0.0068 | 0.0181 | 0.0497 | -0.1035 | 0.0324 | 0.0933 | 0.0024 | 0.0281 | 0.0992 | 0.0186 | 0.0776 | 25.6593 | 62.0537 | 43.4345 | 23 | 0.5674 | 0.0778 | 0.3539 | 0.429 | 0.8294 | 1.8593 | 0.0501 | -0.1092 | -0.1114 | 0.0318 | -0.0003 | 0.0765 | 0.058 | -0.134 | -0.0498 | 0.1078 | -0.0226 | 0.0288 | 0.0869 | 0.0372 | 0.0995 | 20.4595 | 56.0789 | 36.427 | 24 | 3.6269 | 0.6381 | -0.1325 | 0.7037 | -0.5528 | 0.5691 | 0.0165 | 0.1543 | -0.117 | -0.0542 | 0.0138 | -0.0059 | 0.1503 | -0.0275 | -0.0303 | 0.1346 | -0.026 | 0.008 | 0.0632 | -0.0038 | 0.1002 | 21.3971 | 56.0035 | 19.1813 | 25 | 4.5877 | 1.4226 | -4.7287 | 3.2908 | -1.0711 | 5.389 | -0.1004 | -0.0156 | -0.2702 | -0.038 | 0.0033 | -0.0397 | 0.2496 | -0.0268 | 0.0971 | 0.0953 | -0.0227 | 0.002 | 0.0449 | 0.0151 | 0.1249 | 27.2278 | 47.9941 | 27.0622 | 26 | 2.6691 | 1.2029 | 1.3423 | 3.1664 | -0.8637 | 1.1559 | 0.0806 | -0.1326 | -0.089 | 0.0877 | 0.0209 | 0.0334 | 0.0421 | -0.1641 | -0.1015 | 0.0852 | -0.0452 | 0.0268 | 0.1143 | 0.0131 | 0.1002 | 11.1864 | 56.0854 | 32.1419 | 27 | 0.6278 | -0.2157 | 0.0778 | 0.2127 | 0.0888 | 0.6743 | -0.0044 | -0.0293 | -0.0087 | 0.0082 | -0.0047 | -0.0088 | 0.0238 | -0.0405 | 0.0091 | 0.0848 | -0.0086 | 0.0147 | 0.0669 | 0.0028 | 0.0958 | 24.2411 | 64.5795 | 29.0061 | 28 | 1.9053 | 1.9133 | 0.8946 | 5.8492 | -1.3909 | 2.2131 | -0.1483 | -0.0663 | 0.1487 | -0.0392 | 0.1839 | 0.4299 | -0.1279 | -0.3095 | -0.0356 | 0.063 | 0.0229 | -0.0101 | 0.109 | -0.0048 | 0.1139 | 9.8871 | 69.2397 | 24.7463 | 29 | 0.8002 | -0.1351 | 0.2323 | 0.3301 | 0.0762 | 0.304 | -0.0676 | -0.0538 | 0.0926 | 0.0108 | 0.0108 | 0.0223 | -0.0316 | -0.0221 | 0.0567 | 0.0944 | 0.0085 | -0.0008 | 0.0637 | -0.0053 | 0.0847 | 29.7522 | 72.8194 | 30.0085 | 30 | 1.5775 | -0.2849 | -1.4212 | 1.848 | -0.4785 | 2.9816 | -0.0479 | -0.1576 | 0.0796 | 0.075 | 0.0475 | 0.065 | -0.0698 | -0.0703 | 0.0005 | 0.0786 | 0.0427 | 0.004 | 0.1038 | -0.0144 | 0.0715 | 32.1999 | 74.507 | 47.9322 | 31 | 3.4762 | -3.2299 | -0.6968 | 10.878 | -0.2595 | 7.5689 | -0.1577 | -0.5368 | -0.0828 | 0.7771 | 0.1065 | 0.2533 | -0.3019 | -0.354 | 0.0513 | 0.1247 | 0.0688 | 0.0291 | 0.2377 | 0.0267 | 0.008 | 34.5601 | 68.0179 | 60.0519 | 32 | 5.5074 | 5.6771 | -2.8596 | 19.6255 | -9.5791 | 7.0217 | 0.2845 | -0.8056 | 0.19 | 0.718 | -0.0531 | 0.3848 | 0.0045 | 0.2362 | -0.2313 | 0.2648 | 0.0766 | -0.015 | 0.2584 | -0.0492 | 0.0325 | 39.9402 | 71.0605 | 63.2485 | 33 | 1.0706 | -0.4926 | -0.6921 | 0.5188 | 0.2359 | 1.3629 | -0.0786 | -0.103 | 0.1421 | 0.0215 | 0.0533 | -0.036 | -0.0882 | -0.0119 | 0.0253 | 0.089 | 0.0248 | -0.0146 | 0.0837 | -0.0263 | 0.0902 | 44.521 | 77.1882 | 45.2585 | 34 | 3.8647 | 0.2388 | -3.0399 | 2.2909 | 1.2147 | 10.677 | 0.0927 | 0.1839 | 0.5044 | -0.1429 | 0.0275 | 0.0103 | -0.856 | -0.3801 | -0.1201 | 0.1161 | 0.0229 | -0.0353 | 0.0216 | -0.0012 | 0.1468 | 49.2029 | 83.1107 | 39.7896 | 35 | 2.3898 | 0.3491 | 0.8299 | 0.6519 | -0.3612 | 0.6879 | -0.0484 | -0.1759 | 0.1092 | -0.0419 | -0.0275 | 0.0153 | 0.0208 | -0.0171 | 0.0759 | 0.0814 | 0.0293 | -0.0233 | 0.1125 | -0.0184 | 0.0865 | 55.5813 | 72.5644 | 49.3223 | 36 | 13.9398 | 9.0485 | 7.7944 | 21.2987 | 2.7016 | 10.0716 | -0.401 | -0.6859 | 0.7702 | 0.3458 | 0.0043 | 0.3525 | -0.4985 | -0.2915 | 0.3967 | 0.1238 | 0.0632 | -0.0178 | 0.2493 | -0.1407 | 0.1125 | 54.5903 | 78.196 | 58.2246 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A12 - 29 | 2 | X-RAY DIFFRACTION | 2 | A30 - 42 | 3 | X-RAY DIFFRACTION | 3 | A43 - 62 | 4 | X-RAY DIFFRACTION | 4 | A63 - 72 | 5 | X-RAY DIFFRACTION | 5 | A73 - 122 | 6 | X-RAY DIFFRACTION | 6 | A123 - 134 | 7 | X-RAY DIFFRACTION | 7 | A135 - 142 | 8 | X-RAY DIFFRACTION | 8 | A143 - 154 | 9 | X-RAY DIFFRACTION | 9 | A155 - 181 | 10 | X-RAY DIFFRACTION | 10 | A182 - 191 | 11 | X-RAY DIFFRACTION | 11 | A192 - 204 | 12 | X-RAY DIFFRACTION | 12 | A205 - 244 | 13 | X-RAY DIFFRACTION | 13 | A245 - 262 | 14 | X-RAY DIFFRACTION | 14 | A263 - 285 | 15 | X-RAY DIFFRACTION | 15 | A286 - 322 | 16 | X-RAY DIFFRACTION | 16 | A323 - 334 | 17 | X-RAY DIFFRACTION | 17 | A335 - 346 | 18 | X-RAY DIFFRACTION | 18 | A347 - 352 | 19 | X-RAY DIFFRACTION | 19 | B13 - 29 | 20 | X-RAY DIFFRACTION | 20 | B30 - 54 | 21 | X-RAY DIFFRACTION | 21 | B55 - 74 | 22 | X-RAY DIFFRACTION | 22 | B75 - 108 | 23 | X-RAY DIFFRACTION | 23 | B109 - 124 | 24 | X-RAY DIFFRACTION | 24 | B125 - 134 | 25 | X-RAY DIFFRACTION | 25 | B135 - 145 | 26 | X-RAY DIFFRACTION | 26 | B146 - 155 | 27 | X-RAY DIFFRACTION | 27 | B156 - 180 | 28 | X-RAY DIFFRACTION | 28 | B181 - 192 | 29 | X-RAY DIFFRACTION | 29 | B193 - 243 | 30 | X-RAY DIFFRACTION | 30 | B244 - 256 | 31 | X-RAY DIFFRACTION | 31 | B257 - 264 | 32 | X-RAY DIFFRACTION | 32 | B265 - 292 | 33 | X-RAY DIFFRACTION | 33 | B293 - 322 | 34 | X-RAY DIFFRACTION | 34 | B323 - 335 | 35 | X-RAY DIFFRACTION | 35 | B336 - 347 | 36 | X-RAY DIFFRACTION | 36 | B348 - 352 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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