ソフトウェア | 名称 | 分類 |
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autoBUSTER | 精密化 | XDS | データ削減 | SCALA | データスケーリング | PHASER | 位相決定 |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2→29.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.21 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.178
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2549 | 3744 | 5.07 % | RANDOM |
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Rwork | 0.2156 | - | - | - |
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obs | 0.2176 | 73840 | 100 % | - |
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原子変位パラメータ | Biso mean: 53.86 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 5.0637 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -5.3849 Å2 | 0 Å2 |
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3- | - | - | 0.3213 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.3 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2→29.16 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8398 | 0 | 30 | 560 | 8988 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 | Restraint function | Weight |
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X-RAY DIFFRACTION | t_bond_d0.008 | 8598 | HARMONIC2 | X-RAY DIFFRACTION | t_angle_deg0.98 | 11604 | HARMONIC2 | X-RAY DIFFRACTION | t_dihedral_angle_d | 3080 | SINUSOIDAL2 | X-RAY DIFFRACTION | t_incorr_chiral_ct | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_trig_c_planes | | | | X-RAY DIFFRACTION | t_gen_planes | 1433 | HARMONIC5 | X-RAY DIFFRACTION | t_it | 8598 | HARMONIC10 | X-RAY DIFFRACTION | t_nbd | | | | X-RAY DIFFRACTION | t_omega_torsion3.35 | | | | X-RAY DIFFRACTION | t_other_torsion18.29 | | | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion | 1106 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_sum_occupancies | | | | X-RAY DIFFRACTION | t_utility_distance | | | | X-RAY DIFFRACTION | t_utility_angle | | | | X-RAY DIFFRACTION | t_utility_torsion | | | | X-RAY DIFFRACTION | t_ideal_dist_contact | 7404 | SEMIHARMONIC4 | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2→2.01 Å / Total num. of bins used: 51
| Rfactor | 反射数 | %反射 |
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Rfree | 0.392 | - | 5.48 % |
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Rwork | 0.3949 | 1396 | - |
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all | 0.3948 | 1477 | - |
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obs | - | - | 99.87 % |
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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 | 5.2053 | -0.1233 | -1.394 | 10.0471 | 0.3232 | 6.6226 | 0.1152 | -0.0533 | 0.1975 | 0.5438 | 0.0235 | 0.3828 | -0.5466 | 0.0017 | -0.1387 | 0.0341 | -0.0202 | 0.1066 | -0.1186 | -0.0273 | -0.1902 | -15.2083 | 8.3316 | 60.8308 | 2 | 5.5638 | -1.837 | -1.3515 | 13.518 | -0.2882 | 6.3529 | -0.0081 | 0.1829 | -0.3318 | 0.4681 | -0.2562 | 1.3678 | 0.2435 | -0.6183 | 0.2642 | -0.0348 | -0.0612 | 0.1387 | -0.051 | -0.0984 | -0.0625 | -19.8924 | -1.4185 | 55.6991 | 3 | 9.1274 | -2.4154 | 6.8011 | 10.9994 | 0.9842 | 18.7413 | 0.0615 | -0.0546 | -0.6179 | -0.2978 | 0.0632 | 0.7669 | 0.6844 | -0.4783 | -0.1247 | -0.0587 | -0.0556 | 0.1148 | -0.1327 | -0.0591 | -0.0421 | -16.9099 | -7.9816 | 52.4218 | 4 | 1.6804 | -2.5442 | -5.2816 | 6.8219 | 1.9064 | 0.3386 | 0.1182 | -0.0956 | 0.0978 | 0.2144 | -0.0273 | 0.02 | 0.3795 | 0.1929 | -0.091 | 0.0403 | -0.0497 | 0.0645 | -0.0942 | 0.0098 | -0.1685 | -9.2378 | -0.6212 | 52.52 | 5 | 5.521 | 3.0053 | -3.5959 | 9.0598 | 2.8013 | 5.5621 | -0.0569 | -0.2891 | -0.619 | 0.6094 | -0.0837 | -0.0621 | -0.0145 | 0.2668 | 0.1406 | 0.0382 | -0.0202 | 0.0456 | -0.066 | -0.0168 | -0.0885 | -3.8824 | -6.4716 | 48.4319 | 6 | 0 | 1.7243 | -2.2673 | 0 | 2.9249 | 7.1598 | -0.0454 | -0.5197 | 0.0598 | 1.0308 | 0.1405 | -0.12 | -0.2325 | 0.0956 | -0.0952 | 0.162 | -0.1109 | 0.0104 | -0.0247 | -0.019 | -0.1646 | -3.6772 | 7.1857 | 56.0554 | 7 | 1.7565 | 3.4542 | -5.3053 | 12.6069 | -12.8033 | 19.7233 | 0.1214 | 0.0694 | 0.0031 | 0.5022 | 0.1483 | 0.4005 | -0.1694 | -0.2105 | -0.2697 | 0.0283 | 0.0489 | 0.0391 | -0.0419 | -0.0241 | -0.1185 | -10.7184 | 15.1448 | 42.4772 | 8 | 14.7806 | 3.5539 | -12.2255 | 5.1918 | -5.1614 | 13.0156 | 0.1641 | 0.3892 | 0.8997 | 0.1814 | 0.4428 | 0.4183 | -0.3468 | -0.4496 | -0.6069 | 0.0026 | -0.0374 | -0.0236 | -0.1337 | -0.0175 | -0.1036 | -1.3891 | 28.959 | 25.3064 | 9 | 4.7289 | 0.0745 | -7.7984 | 0.4704 | 1.263 | 13.5147 | 0.1679 | -0.1259 | 0.4488 | 0.1769 | 0.3791 | -0.2475 | 0.0747 | 0.4274 | -0.5469 | -0.041 | -0.0313 | -0.0685 | -0.0389 | -0.0302 | -0.0287 | 2.6871 | 20.1064 | 19.3834 | 10 | 16.5877 | 3.5442 | -4.8931 | 23.4435 | -3.8681 | 10.9744 | -0.3314 | -0.2085 | -0.6389 | 0.5252 | 0.536 | 2.1496 | 0.5141 | -2.0024 | -0.2046 | -0.1214 | 0.0076 | -0.0216 | 0.1995 | 0.0523 | 0.124 | -12.0739 | 23.6258 | 23.671 | 11 | 7.698 | -1.7337 | -2.2244 | 5.4701 | 1.3984 | 4.9682 | 0.1796 | -0.0047 | 1.156 | -0.4559 | 0.2276 | -0.654 | -0.7238 | 0.6572 | -0.4072 | -0.0428 | -0.2087 | -0.0044 | 0.0495 | 0.0451 | -0.079 | 7.7942 | 22.2813 | 4.4585 | 12 | 0.0131 | -1.3827 | 0.1141 | 4.6346 | -0.8203 | 0.3587 | -0.0829 | 0.3011 | -0.0868 | -0.1949 | -0.105 | -0.6974 | -0.0604 | 0.6577 | 0.1879 | -0.1627 | -0.0437 | 0.0062 | 0.0931 | -0.0332 | 0.0742 | 15.4912 | 3.046 | 9.3761 | 13 | 1.5582 | 0.0734 | -0.0802 | 2.0231 | -0.6086 | 0.6309 | -0.0806 | 0.1183 | -0.0743 | -0.3332 | 0.0432 | -0.1618 | 0.0112 | 0.1732 | 0.0375 | -0.0896 | -0.0409 | 0.0157 | 0.0256 | -0.0368 | -0.0578 | 4.8088 | 1.7561 | 5.7572 | 14 | 6.701 | 1.7201 | 0.2304 | 3.3943 | -0.6145 | 0.6017 | -0.1354 | 0.6569 | -1.256 | -0.3507 | -0.0377 | -0.4019 | 0.3372 | 0.0427 | 0.1731 | -0.0607 | 0.0428 | 0.0573 | 0.0014 | -0.0876 | -0.0522 | 5.7046 | -9.9462 | 6.402 | 15 | 5.1297 | -3.6074 | 1.6443 | 5.207 | -1.1765 | 1.7078 | -0.0316 | 0.2103 | -0.5215 | -0.1725 | 0.1141 | 0.2049 | 0.0947 | 0.043 | -0.0825 | -0.0534 | -0.0532 | 0.0059 | -0.02 | -0.0248 | -0.0742 | -4.1989 | -5.5578 | 10.4116 | 16 | 3.7018 | -2.4795 | 0.7628 | 3.6364 | -1.439 | 1.3475 | -0.0358 | -0.0984 | 0.0163 | 0.1681 | 0.0688 | 0.085 | -0.1096 | 0.0159 | -0.0331 | -0.1108 | -0.0372 | -0.0079 | 0.0141 | 0.0007 | -0.0255 | -12.5488 | 3.9185 | 17.6783 | 17 | 2.2859 | -2.1904 | 1.5236 | 4.9411 | -2.2167 | 1.8835 | 0.0306 | 0.1501 | -0.1771 | -0.3919 | -0.0365 | -0.0325 | 0.1033 | 0.1908 | 0.0059 | -0.0939 | -0.0426 | -0.0268 | 0.0157 | -0.0194 | -0.0701 | -2.1224 | 3.5972 | 10.3733 | 18 | 13.022 | -2.6908 | 0.7261 | 8.219 | -1.6706 | 10.0427 | 0.2957 | 1.4698 | -0.5366 | -1.489 | -0.7332 | -0.1744 | 0.0313 | 0.0716 | 0.4375 | 0.1968 | 0.0424 | -0.0894 | 0.04 | -0.0174 | -0.2209 | -5.7447 | 16.787 | -8.7731 | 19 | 9.2613 | -1.7355 | -0.1678 | 1.7581 | -0.3651 | 1.2658 | 0.1208 | 1.3033 | 0.1616 | -0.7033 | -0.1414 | 0.0019 | -0.3382 | 0.1856 | 0.0206 | 0.2148 | -0.1191 | -0.0348 | 0.0905 | 0.0776 | -0.1985 | -1.7171 | 18.6686 | -7.5421 | 20 | 1.9757 | -0.674 | 1.4277 | 2.9215 | -1.333 | 2.0686 | -0.0945 | -0.1543 | 0.099 | -0.2885 | 0.0852 | 0.0229 | -0.0669 | 0.0488 | 0.0093 | -0.0589 | -0.0417 | -0.015 | -0.0262 | -0.0139 | -0.1073 | -6.3346 | 11.3379 | 7.5281 | 21 | 4.7341 | 1.2116 | 0.1471 | 9.0142 | -2.4739 | 5.7421 | -0.0432 | -0.42 | -0.7078 | 0.379 | -0.076 | -0.8449 | -0.1932 | 0.6936 | 0.1192 | -0.1762 | -0.0398 | -0.055 | 0.0518 | 0.0817 | -0.0108 | 15.0891 | 5.6245 | 46.5218 | 22 | 4.5553 | 0.5869 | -0.5758 | 9.4279 | -1.6526 | 5.256 | -0.1215 | 0.2022 | -0.1787 | 0.0782 | -0.0236 | -0.2854 | -0.121 | 0.3511 | 0.1451 | -0.1228 | -0.1065 | -0.0223 | -0.0014 | 0.0223 | -0.1667 | 12.255 | 12.2343 | 39.1601 | 23 | 0.5989 | 1.2758 | -1.6063 | 0 | -2.354 | 9.4516 | -0.0082 | 0.1303 | 0.2186 | 0.1417 | -0.1915 | 0.1698 | -0.4336 | -0.3264 | 0.1997 | 0.0439 | -0.0734 | -0.0746 | 0.0532 | 0.0179 | -0.0834 | 4.8981 | 12.6751 | 38.6386 | 24 | 10.2339 | -3.1509 | -3.0359 | 5.3724 | 0.1513 | 10.5141 | 0.4154 | -0.3996 | 0.8306 | 1.1493 | -0.5673 | 0.3356 | -0.8892 | 0.3731 | 0.1519 | 0.1688 | -0.1113 | 0.0452 | -0.1411 | -0.0368 | -0.0099 | -2.5945 | 20.8031 | 50.8192 | 25 | 10.6389 | -8.3472 | 0.6958 | 18.5623 | 2.8146 | 6.1966 | 0.2116 | 0.4379 | 0.3433 | -0.1698 | -0.204 | 0.0147 | -0.0188 | 0.2786 | -0.0076 | 0.0008 | -0.0804 | 0.0205 | -0.0185 | 0.0471 | -0.1212 | -3.0357 | 15.1919 | 41.5022 | 26 | 1.9353 | 1.9426 | -1.1316 | 10.7736 | 3.2083 | 5.3693 | -0.0069 | -0.1476 | -0.3217 | 0.2876 | 0.0162 | -0.3481 | -0.3749 | 0.529 | -0.0092 | -0.0444 | -0.051 | -0.0336 | 0.0091 | 0.0469 | -0.0999 | 3.6449 | 4.0509 | 49.1249 | 27 | 15.9205 | 12.4144 | 2.2558 | 10.4565 | 0.4499 | 2.8574 | 0.3533 | -0.4325 | -0.0959 | 0.2769 | -0.1097 | -0.0541 | 0.2144 | -0.0011 | -0.2436 | 0.005 | 0.0577 | 0.0145 | -0.0218 | -0.0014 | -0.1079 | -13.2888 | -16.26 | 40.2948 | 28 | 8.1758 | 1.4647 | 2.7456 | 0.0027 | 0.0109 | 1.7936 | 0.0135 | -0.8339 | -0.3983 | 0.1736 | 0.0224 | -0.1671 | 0.2697 | -0.4181 | -0.0358 | 0.0417 | 0.0257 | 0.0163 | 0.0534 | 0.0588 | -0.073 | -29.8622 | -14.3454 | 37.5332 | 29 | 10.0736 | -1.4128 | 1.9223 | 2.1674 | 0.1537 | 2.0251 | 0.218 | 0.0708 | -0.6894 | 0.1153 | -0.0395 | 0.2876 | 0.3154 | -0.1622 | -0.1785 | -0.0456 | -0.0624 | 0.0384 | -0.0585 | 0.0618 | -0.1612 | -31.9712 | -17.5239 | 31.1949 | 30 | 1.8361 | 2.0933 | -0.1775 | 1.5166 | 3.0468 | 6.9301 | 0.0047 | -0.0334 | 0.3228 | 0.9584 | -0.1439 | 1.1476 | 0.1192 | -0.7771 | 0.1392 | -0.1435 | 0.0755 | 0.1265 | 0.0598 | -0.0359 | 0.1027 | -46.491 | 3.7908 | 34.2231 | 31 | 3.3761 | 1.2587 | -0.3435 | 1.9093 | -0.6864 | 1.057 | 0.0402 | -0.1526 | 0.1795 | 0.3227 | 0.0171 | 0.3478 | -0.1402 | -0.1184 | -0.0573 | -0.127 | 0.0609 | 0.0413 | 0.0416 | -0.0038 | -0.0054 | -35.812 | 0.8804 | 28.6314 | 32 | 1.2637 | 0.055 | 3.6141 | 4.9298 | 0.2751 | 0.2083 | 0.1364 | -0.1951 | 0.3278 | -0.1476 | -0.2345 | 0.8966 | -0.3532 | -0.4419 | 0.0981 | -0.2767 | 0.0151 | -0.0769 | 0.1814 | 0.047 | 0.184 | -53.2629 | -2.6763 | 14.1455 | 33 | 6.0041 | -1.55 | -2.0059 | 8.3249 | 4.0166 | 10.8531 | -0.023 | 1.0242 | 0.7156 | -0.4991 | -0.1072 | 1.1166 | -0.4989 | -0.9978 | 0.1303 | -0.3737 | 0.0292 | -0.0737 | 0.0718 | 0.1059 | 0.295 | -49.5549 | 4.6925 | 18.3516 | 34 | 6.5591 | -0.5383 | -1.9384 | 6.2592 | 0.2955 | 3.1466 | -0.047 | 0.4769 | 1.0029 | -0.1821 | 0.0646 | 0.8262 | -0.3938 | -0.1565 | -0.0176 | -0.1913 | 0.0786 | -0.0461 | -0.0835 | 0.0746 | 0.206 | -37.2574 | 14.7491 | 21.7281 | 35 | 4.8076 | -2.3594 | -2.2076 | 8.3455 | 4.1841 | 8.3704 | -0.014 | 0.6701 | 0.401 | -0.5168 | -0.0762 | 0.0602 | -0.0386 | -0.5174 | 0.0902 | -0.099 | 0.0003 | -0.0337 | 0.046 | 0.0248 | -0.043 | -24.0731 | -4.0752 | 11.9151 | 36 | 2.6888 | -0.8676 | -1.0142 | 1.2093 | 1.1554 | 0 | -0.0514 | -0.1296 | -0.0156 | 0.2047 | -0.0817 | 0.1143 | -0.1091 | 0.1504 | 0.1331 | -0.0734 | 0.0182 | -0.0055 | 0.0627 | 0.0118 | -0.0302 | -19.9548 | 0.2574 | 21.6068 | 37 | 2.5234 | 0.5749 | -0.4947 | 7.3994 | 2.1506 | 1.6228 | 0.023 | 0.0601 | 0.3496 | 0.1634 | 0.0363 | 0.2629 | 0.0265 | -0.0833 | -0.0594 | -0.1743 | 0.054 | -0.0305 | 0.0113 | 0.0398 | -0.0909 | -32.0338 | 0.1148 | 23.7932 | 38 | 13.5491 | 0.5014 | 0.5564 | 11.8324 | -3.3031 | 5.8797 | -0.2288 | 1.6131 | -0.7537 | -1.4723 | -0.0875 | 0.8006 | 0.6707 | -0.9063 | 0.3163 | -0.1316 | -0.1094 | -0.0174 | 0.1694 | -0.2362 | -0.0069 | -40.9075 | -21.1281 | 13.5946 | 39 | 5.0291 | -1.8965 | -5.4998 | 4.2444 | 1.5061 | 4.2046 | -0.367 | 1.3548 | -0.6076 | -0.5549 | -0.057 | 0.7034 | 0.4419 | -1.0973 | 0.424 | -0.1127 | -0.1368 | -0.0905 | 0.1857 | -0.0789 | 0.0835 | -40.9641 | -19.2727 | 12.7915 | 40 | 1.8942 | 0.1241 | -1.012 | 2.1899 | 1.4248 | 5.4872 | -0.0034 | -0.0759 | -0.0114 | 0.1069 | 0.003 | 0.2135 | 0.0628 | -0.0116 | 0.0003 | -0.1791 | -0.0044 | -0.0072 | 0.0126 | 0.0221 | -0.0651 | -31.2394 | -6.2455 | 24.5787 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | { A|2 - 34 } | 2 | X-RAY DIFFRACTION | 2 | { A|35 - 56 } | 3 | X-RAY DIFFRACTION | 3 | { A|57 - 73 } | 4 | X-RAY DIFFRACTION | 4 | { A|74 - 85 } | 5 | X-RAY DIFFRACTION | 5 | { A|86 - 100 } | 6 | X-RAY DIFFRACTION | 6 | { A|101 - 113 } | 7 | X-RAY DIFFRACTION | 7 | { A|114 - 128 } | 8 | X-RAY DIFFRACTION | 8 | { A|129 - 147 } | 9 | X-RAY DIFFRACTION | 9 | { A|148 - 167 } | 10 | X-RAY DIFFRACTION | 10 | { A|168 - 182 } | 11 | X-RAY DIFFRACTION | 11 | { A|183 - 208 } | 12 | X-RAY DIFFRACTION | 12 | { A|209 - 226 } | 13 | X-RAY DIFFRACTION | 13 | { A|227 - 314 } | 14 | X-RAY DIFFRACTION | 14 | { A|315 - 339 } | 15 | X-RAY DIFFRACTION | 15 | { A|340 - 370 } | 16 | X-RAY DIFFRACTION | 16 | { A|371 - 396 } | 17 | X-RAY DIFFRACTION | 17 | { A|397 - 429 } | 18 | X-RAY DIFFRACTION | 18 | { A|434 - 447 } | 19 | X-RAY DIFFRACTION | 19 | { A|448 - 485 } | 20 | X-RAY DIFFRACTION | 20 | { A|486 - 517 } | 21 | X-RAY DIFFRACTION | 21 | { B|2 - 24 } | 22 | X-RAY DIFFRACTION | 22 | { B|25 - 69 } | 23 | X-RAY DIFFRACTION | 23 | { B|70 - 84 } | 24 | X-RAY DIFFRACTION | 24 | { B|85 - 90 } | 25 | X-RAY DIFFRACTION | 25 | { B|91 - 100 } | 26 | X-RAY DIFFRACTION | 26 | { B|101 - 119 } | 27 | X-RAY DIFFRACTION | 27 | { B|120 - 144 } | 28 | X-RAY DIFFRACTION | 28 | { B|145 - 165 } | 29 | X-RAY DIFFRACTION | 29 | { B|166 - 210 } | 30 | X-RAY DIFFRACTION | 30 | { B|211 - 227 } | 31 | X-RAY DIFFRACTION | 31 | { B|228 - 285 } | 32 | X-RAY DIFFRACTION | 32 | { B|286 - 299 } | 33 | X-RAY DIFFRACTION | 33 | { B|300 - 320 } | 34 | X-RAY DIFFRACTION | 34 | { B|321 - 358 } | 35 | X-RAY DIFFRACTION | 35 | { B|359 - 371 } | 36 | X-RAY DIFFRACTION | 36 | { B|372 - 396 } | 37 | X-RAY DIFFRACTION | 37 | { B|397 - 428 } | 38 | X-RAY DIFFRACTION | 38 | { B|435 - 452 } | 39 | X-RAY DIFFRACTION | 39 | { B|453 - 491 } | 40 | X-RAY DIFFRACTION | 40 | { B|492 - 517 } |
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