ソフトウェア | 名称 | バージョン | 分類 |
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Blu-Ice | Maxデータ収集 | PHENIX | | モデル構築 | REFMAC | 5.8.0046精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHENIX | | 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: 2.22→28.63 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.842 / SU ML: 0.18 Isotropic thermal model: Thermal Factors Individually Isotropically Refined 交差検証法: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.247 / 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 | 0.24143 | 2697 | 5.1 % | RANDOM |
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Rwork | 0.18125 | - | - | - |
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obs | 0.18431 | 50666 | 98.13 % | - |
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all | - | 50666 | - | - |
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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: 28.821 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.14 Å2 | -1.03 Å2 | 0.02 Å2 |
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2- | - | -1.82 Å2 | 0.36 Å2 |
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3- | - | - | 1 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.22→28.63 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 9482 | 0 | 7 | 597 | 10086 |
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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_d0.011 | 0.019 | 9906 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 9239 | X-RAY DIFFRACTION | r_angle_refined_deg1.566 | 1.958 | 13481 | X-RAY DIFFRACTION | r_angle_other_deg0.792 | 3 | 21245 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg3.178 | 5 | 1232 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg29.455 | 23.099 | 455 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.051 | 15 | 1484 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.681 | 15 | 71 | X-RAY DIFFRACTION | r_chiral_restr0.093 | 0.2 | 1463 | X-RAY DIFFRACTION | r_gen_planes_refined0.02 | 0.021 | 11342 | X-RAY DIFFRACTION | r_gen_planes_other0.017 | 0.02 | 2393 | X-RAY DIFFRACTION | r_mcbond_it1.312 | 1.267 | 4904 | X-RAY DIFFRACTION | r_mcbond_other1.312 | 1.267 | 4903 | X-RAY DIFFRACTION | r_mcangle_it1.394 | 1.894 | 6140 | X-RAY DIFFRACTION | r_mcangle_other1.394 | 1.894 | 6141 | X-RAY DIFFRACTION | r_scbond_it1.513 | 1.431 | 5002 | X-RAY DIFFRACTION | r_scbond_other1.513 | 1.431 | 5002 | X-RAY DIFFRACTION | r_scangle_other2.1 | 2.085 | 7341 | X-RAY DIFFRACTION | r_long_range_B_refined5.106 | 11.317 | 11884 | X-RAY DIFFRACTION | r_long_range_B_other5.002 | 11.049 | 11693 | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.22→2.277 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.313 | 198 | - |
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Rwork | 0.232 | 3600 | - |
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obs | - | 3600 | 94.5 % |
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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 | 9.672 | -0.142 | -0.8157 | 1.8978 | -0.5699 | 3.3526 | 0.3974 | -0.7031 | -0.9321 | 0.4591 | -0.4269 | -0.5759 | 0.1123 | 0.1582 | 0.0295 | 0.4219 | -0.0039 | -0.1843 | 0.3884 | 0.11 | 0.346 | 45.5108 | 42.0117 | 99.5046 | 2 | 0.4618 | 0.3193 | 0.3967 | 1.0213 | 0.2172 | 1.7704 | 0.0551 | -0.0838 | -0.0205 | 0.0474 | 0.0431 | 0.0496 | -0.1253 | -0.2731 | -0.0982 | 0.0779 | 0.0693 | -0.0097 | 0.1397 | -0.0071 | 0.0202 | 36.7255 | 44.5018 | 83.5337 | 3 | 1.6494 | 5.6195 | -0.378 | 19.3131 | -1.3339 | 0.1006 | -0.6793 | 0.2972 | 0.691 | -2.1196 | 0.7693 | 2.0362 | 0.0916 | -0.0033 | -0.09 | 0.7586 | -0.1832 | -0.536 | 0.8238 | 0.328 | 1.0679 | 52.0839 | 47.9482 | 73.333 | 4 | 0.4055 | -0.1052 | 0.1442 | 0.8844 | -0.1641 | 1.4978 | -0.0208 | -0 | 0.0338 | -0.0235 | 0.1141 | -0.0113 | -0.349 | -0.1897 | -0.0932 | 0.1438 | 0.1015 | 0.0141 | 0.1515 | -0.0171 | 0.0199 | 37.8853 | 51.9366 | 79.527 | 5 | 13.6364 | -5.0468 | 4.1635 | 4.3516 | -4.4935 | 6.9267 | 0.0113 | 0.5177 | 0.394 | -0.4097 | -0.1723 | -0.4084 | -0.0338 | -0.1698 | 0.1611 | 0.2475 | 0.046 | 0.0873 | 0.2004 | 0.0173 | 0.0922 | 24.0089 | -1.2089 | 35.4957 | 6 | 0.4155 | -0.1496 | -0.1825 | 1.0839 | 0.3305 | 1.8383 | 0.0333 | 0.066 | 0.035 | -0.0309 | -0.0056 | 0.0939 | 0.1051 | -0.2115 | -0.0276 | 0.0644 | -0.0034 | -0.0038 | 0.1163 | -0.0184 | 0.0257 | 13.2809 | -2.9221 | 50.7869 | 7 | 17.5616 | -15.2731 | -10.5632 | 13.727 | 9.027 | 6.4112 | -1.5313 | -0.658 | -2.4402 | 1.3644 | 0.0719 | 2.0842 | 0.8814 | 0.5659 | 1.4594 | 0.5227 | -0.0055 | 0.1351 | 0.5614 | 0.072 | 0.4886 | 28.198 | -6.5665 | 61.7177 | 8 | 0.598 | 0.1477 | -0.125 | 1.2215 | 0.1446 | 1.4423 | 0.0155 | -0.0213 | -0.0162 | 0.0597 | 0.02 | 0.0205 | 0.3297 | -0.1668 | -0.0355 | 0.1375 | -0.0262 | -0.0228 | 0.1294 | -0.0299 | 0.0161 | 14.0616 | -10.4804 | 55.526 | 9 | 4.6288 | -0.6556 | -0.6064 | 2.7611 | 1.1947 | 5.5986 | 0.0658 | 0.1297 | -0.4956 | -0.5502 | 0.1425 | -0.7135 | -0.0255 | 0.4885 | -0.2083 | 0.2732 | 0.0462 | 0.0881 | 0.3654 | -0.1237 | 0.3177 | 49.5639 | 18.7839 | 35.3913 | 10 | 0.7609 | 0.0486 | -0.3616 | 3.2642 | 0.7984 | 4.7642 | 0.0709 | 0.1445 | -0.1477 | -0.4113 | 0.13 | -0.1349 | -0.0307 | 0.0054 | -0.2008 | 0.1467 | -0.0107 | -0.0064 | 0.1421 | -0.0586 | 0.0519 | 38.7052 | 19.6915 | 38.0152 | 11 | 0.3955 | -0.1294 | 0.0988 | 1.0417 | 0.9033 | 1.7149 | -0.0465 | 0.0895 | -0.0329 | -0.3147 | 0.1082 | -0.0814 | -0.4006 | 0.1292 | -0.0618 | 0.1818 | -0.04 | 0.0196 | 0.1042 | -0.046 | 0.0229 | 40.3946 | 32.1824 | 47.3301 | 12 | 1.6233 | -0.8395 | 0.2121 | 1.5364 | 0.2701 | 3.1776 | 0.0665 | 0.0273 | -0.1094 | -0.1638 | -0.0724 | 0.3323 | -0.4833 | -0.4143 | 0.0059 | 0.2431 | 0.0591 | -0.0773 | 0.2294 | -0.0376 | 0.1014 | 24.4983 | 30.7558 | 43.6114 | 13 | 8.8823 | -2.5953 | 4.8863 | 8.1526 | -6.3467 | 21.3703 | -0.055 | 0.105 | -0.2265 | -0.4926 | 0.255 | 0.3795 | -0.2897 | -0.5405 | -0.2 | 0.1215 | 0.0245 | -0.0693 | 0.114 | -0.0667 | 0.0864 | 24.07 | 20.7205 | 34.6121 | 14 | 14.8227 | -7.0097 | 11.6844 | 6.7053 | -4.3473 | 9.9366 | -0.0542 | 0.1745 | -0.7983 | 0.1769 | 0.4942 | -0.2056 | -0.308 | 0.5204 | -0.44 | 0.5116 | -0.1214 | -0.1717 | 0.4544 | 0.0545 | 0.6342 | 23.3873 | 28.8001 | 97.7793 | 15 | 1.5643 | -0.4171 | 0.3203 | 1.3412 | 0.0733 | 3.7597 | 0.0176 | -0.1167 | 0.213 | 0.2417 | 0.0522 | -0.1881 | -0.0134 | 0.2398 | -0.0699 | 0.1361 | 0.0611 | -0.0315 | 0.1416 | -0.051 | 0.052 | 18.3174 | 20.4932 | 97.1967 | 16 | 0.8227 | 0.2738 | -0.4325 | 0.8795 | 0.9892 | 1.9969 | -0.0969 | -0.0863 | -0.0573 | 0.3276 | 0.0631 | -0.054 | 0.6272 | 0.1033 | 0.0338 | 0.3024 | 0.1052 | -0.01 | 0.1194 | -0.0403 | 0.0284 | 15.7522 | 6.9418 | 89.7262 | 17 | 0.3628 | -0.4879 | -0.2298 | 1.1188 | -0.0783 | 2.8689 | -0.0398 | -0.0454 | 0.0738 | 0.075 | 0.0802 | -0.0402 | 0.4076 | 0.085 | -0.0404 | 0.1276 | 0.0657 | -0.0179 | 0.0915 | -0.0415 | 0.0396 | 16.3277 | 12.4359 | 84.4455 | 18 | 1.1336 | 0.9814 | 0.2562 | 1.447 | 0.6572 | 3.4389 | 0.0775 | 0.0164 | 0.2053 | 0.1316 | -0.0442 | 0.3927 | 0.6362 | -0.4765 | -0.0333 | 0.3007 | -0.023 | 0.0308 | 0.3143 | -0.0319 | 0.1571 | 0.2744 | 10.7185 | 90.7742 | 19 | 4.9694 | 1.7518 | -1.7145 | 7.6688 | -4.8538 | 20.2713 | -0.0189 | -0.0413 | 0.1181 | 0.6165 | 0.346 | 0.563 | -0.4537 | -0.8889 | -0.3271 | 0.0895 | 0.0577 | 0.041 | 0.1629 | -0.0408 | 0.0802 | -0.2447 | 20.4873 | 100.1924 |
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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 | A3 - 22 | 2 | X-RAY DIFFRACTION | 2 | A23 - 185 | 3 | X-RAY DIFFRACTION | 3 | A186 - 198 | 4 | X-RAY DIFFRACTION | 4 | A199 - 304 | 5 | X-RAY DIFFRACTION | 5 | B3 - 15 | 6 | X-RAY DIFFRACTION | 6 | B16 - 185 | 7 | X-RAY DIFFRACTION | 7 | B186 - 198 | 8 | X-RAY DIFFRACTION | 8 | B199 - 304 | 9 | X-RAY DIFFRACTION | 9 | C4 - 29 | 10 | X-RAY DIFFRACTION | 10 | C30 - 72 | 11 | X-RAY DIFFRACTION | 11 | C73 - 242 | 12 | X-RAY DIFFRACTION | 12 | C243 - 289 | 13 | X-RAY DIFFRACTION | 13 | C290 - 304 | 14 | X-RAY DIFFRACTION | 14 | D4 - 14 | 15 | X-RAY DIFFRACTION | 15 | D15 - 79 | 16 | X-RAY DIFFRACTION | 16 | D80 - 182 | 17 | X-RAY DIFFRACTION | 17 | D183 - 243 | 18 | X-RAY DIFFRACTION | 18 | D244 - 289 | 19 | X-RAY DIFFRACTION | 19 | D290 - 304 | | | | | | | | | | | | | | | | | | | |
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