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 | CRANK | | 位相決定 | REFMAC | 5.5.0088精密化 | HKL-2000 | | データ削減 | HKL-2000 | | 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: 2.22→29.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.691 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: Individual Isotropic Temperature Factors Refined 交差検証法: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.146 / 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 | 0.18094 | 5227 | 5 % | RANDOM |
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Rwork | 0.14378 | - | - | - |
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all | 0.14565 | 99164 | - | - |
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obs | 0.14565 | 99164 | 99.79 % | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 15.161 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.91 Å2 | -0 Å2 | -0 Å2 |
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2- | - | 0.91 Å2 | 0 Å2 |
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3- | - | - | -1.82 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.22→29.76 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 11290 | 0 | 3 | 1134 | 12427 |
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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_d0.012 | 0.022 | 11792 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 8059 | X-RAY DIFFRACTION | r_angle_refined_deg1.399 | 1.943 | 16015 | X-RAY DIFFRACTION | r_angle_other_deg0.886 | 3 | 19450 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg2.462 | 5 | 1444 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg31.816 | 23.52 | 608 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg9.355 | 15 | 1984 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg13.427 | 15 | 106 | X-RAY DIFFRACTION | r_chiral_restr0.091 | 0.2 | 1706 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.021 | 13381 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 2576 | X-RAY DIFFRACTION | r_mcbond_it0.877 | 1.5 | 7120 | X-RAY DIFFRACTION | r_mcbond_other0.251 | 1.5 | 2898 | X-RAY DIFFRACTION | r_mcangle_it1.595 | 2 | 11467 | X-RAY DIFFRACTION | r_scbond_it2.993 | 3 | 4672 | X-RAY DIFFRACTION | r_scangle_it4.586 | 4.5 | 4548 | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.22→2.282 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.264 | 386 | - |
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Rwork | 0.213 | 7045 | - |
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obs | - | 7045 | 97.67 % |
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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 | 0.8908 | -0.3559 | -0.3561 | 0.8563 | 0.2892 | 0.4722 | 0.0257 | 0.1022 | -0.0119 | -0.0975 | -0.0389 | -0.0149 | -0.0421 | 0.0121 | 0.0132 | 0.047 | 0.0178 | 0.0298 | 0.0303 | 0.0116 | 0.0462 | 93.8893 | 17.2501 | -3.6426 | 2 | 1.6203 | 0.118 | -0.5035 | 0.9252 | -0.0228 | 0.7101 | 0.0048 | 0.1489 | -0.1156 | -0.0818 | -0.0332 | -0.0285 | -0.0277 | -0.0369 | 0.0285 | 0.0673 | 0.0516 | 0.0213 | 0.0633 | -0.0077 | 0.0366 | 90.8414 | 5.3869 | -8.7502 | 3 | 1.7088 | -0.2579 | 0.1046 | 0.9373 | -0.5121 | 1.9869 | -0.0202 | -0.0107 | -0.0799 | 0.0253 | -0.0268 | -0.1316 | 0.0288 | 0.0643 | 0.047 | 0.0054 | 0.0046 | -0.0136 | 0.0069 | -0.0075 | 0.0575 | 99.0214 | 8.7606 | 23.1609 | 4 | 0.8528 | -0.184 | 0.2092 | 0.6672 | -0.0235 | 0.8804 | -0.0394 | -0.1245 | -0.0452 | 0.0618 | 0.0012 | -0.0266 | -0.0467 | -0.0387 | 0.0382 | 0.0424 | 0.0364 | 0.0072 | 0.0548 | 0.0066 | 0.0368 | 82.583 | 14.897 | 21.4636 | 5 | 1.8219 | -0.7021 | -0.2609 | 0.7523 | -0.1465 | 0.861 | 0.0584 | 0.0591 | 0.2211 | -0.0385 | -0.0884 | -0.1021 | -0.1672 | -0.0163 | 0.0301 | 0.0611 | 0.0248 | 0.0126 | 0.0196 | 0.0165 | 0.0483 | 88.1678 | 29.4141 | 3.1017 | 6 | 0.8808 | -0.002 | 0.1047 | 0.8663 | -0.0324 | 0.6874 | 0.038 | 0.0173 | 0.1863 | 0.0654 | -0.0287 | -0.1245 | -0.2256 | -0.0274 | -0.0093 | 0.1866 | 0.1076 | 0.0123 | 0.0979 | 0.0025 | 0.1543 | 65.0521 | 49.627 | 9.6807 | 7 | 1.0743 | -0.4492 | 0.0919 | 1.0801 | 0.0459 | 1.3417 | 0.02 | -0.0203 | 0.3435 | 0.075 | 0.0235 | -0.2508 | -0.174 | 0.0899 | -0.0434 | 0.193 | 0.0473 | -0.0016 | 0.029 | -0.0209 | 0.1894 | 77.1394 | 51.2869 | 14.8109 | 8 | 0.9961 | -0.5292 | -0.1908 | 3.2879 | -1.5133 | 2.3208 | -0.048 | -0.1855 | 0.1063 | 0.2077 | 0.0254 | -0.0153 | -0.2504 | 0.0393 | 0.0226 | 0.1357 | 0.113 | -0.0042 | 0.1592 | -0.05 | 0.0806 | 55.2872 | 43.4235 | 31.1127 | 9 | 0.7865 | -0.2582 | -0.2041 | 0.4614 | 0.1796 | 0.4976 | -0.0358 | -0.1082 | -0.0298 | 0.1238 | 0.0487 | 0.0535 | -0.0544 | -0.0708 | -0.0129 | 0.126 | 0.1044 | 0.0143 | 0.117 | -0.0018 | 0.0486 | 54.9853 | 28.9253 | 26.821 | 10 | 1.0025 | -0.0273 | 0.1212 | 1.1398 | 0.1883 | 0.506 | 0.0718 | 0.0789 | 0.0311 | -0.0523 | -0.0836 | 0.0212 | -0.1106 | -0.1059 | 0.0118 | 0.1254 | 0.123 | 0.0161 | 0.1242 | 0.0029 | 0.068 | 55.9395 | 39.2109 | 3.5799 | 11 | 1.9131 | -0.4156 | 0.0011 | 0.7898 | 0.2968 | 0.7967 | 0.1372 | 0.2205 | -0.2254 | -0.1211 | -0.1751 | 0.2075 | -0.1176 | -0.2434 | 0.0379 | 0.0967 | 0.1275 | -0.059 | 0.2002 | -0.1007 | 0.1118 | 49.9613 | 13.0387 | -13.4988 | 12 | 1.4266 | -0.4769 | -0.4223 | 0.9259 | 0.4006 | 1.4506 | 0.1441 | 0.2581 | -0.1626 | -0.0751 | -0.115 | 0.194 | -0.0689 | -0.287 | -0.0292 | 0.0724 | 0.1105 | -0.0576 | 0.1973 | -0.0611 | 0.1063 | 39.8328 | 20.9022 | -8.4404 | 13 | 1.9418 | -0.4128 | 0.8516 | 1.5327 | 0.0658 | 2.4708 | 0.052 | -0.1756 | -0.4481 | 0.1048 | -0.0145 | 0.4134 | 0.1958 | -0.4011 | -0.0375 | 0.0389 | -0.0396 | 0.0721 | 0.1095 | -0.0197 | 0.3541 | 49.1163 | -7.8525 | 9.2718 | 14 | 0.9533 | -0.4991 | -0.1118 | 0.626 | -0.0496 | 0.453 | 0.0035 | 0.0462 | -0.2381 | -0.0067 | -0.0527 | 0.1963 | 0.0641 | -0.1063 | 0.0491 | 0.0483 | 0.0164 | 0.0045 | 0.0628 | -0.0343 | 0.1024 | 60.4825 | 4.6507 | 6.8605 | 15 | 2.2263 | 0.5816 | -0.2396 | 1.5505 | -0.433 | 1.1483 | 0.0565 | 0.2429 | -0.0956 | -0.1399 | -0.1355 | 0.0117 | -0.0078 | -0.1004 | 0.079 | 0.0893 | 0.0918 | -0.0397 | 0.1303 | -0.0682 | 0.0531 | 62.9216 | 9.6097 | -12.7176 |
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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 | A2 - 59 | 2 | X-RAY DIFFRACTION | 2 | A60 - 152 | 3 | X-RAY DIFFRACTION | 3 | A153 - 235 | 4 | X-RAY DIFFRACTION | 4 | A236 - 395 | 5 | X-RAY DIFFRACTION | 5 | A396 - 470 | 6 | X-RAY DIFFRACTION | 6 | B2 - 58 | 7 | X-RAY DIFFRACTION | 7 | B59 - 152 | 8 | X-RAY DIFFRACTION | 8 | B153 - 204 | 9 | X-RAY DIFFRACTION | 9 | B205 - 394 | 10 | X-RAY DIFFRACTION | 10 | B395 - 470 | 11 | X-RAY DIFFRACTION | 11 | C3 - 58 | 12 | X-RAY DIFFRACTION | 12 | C59 - 152 | 13 | X-RAY DIFFRACTION | 13 | C153 - 272 | 14 | X-RAY DIFFRACTION | 14 | C273 - 404 | 15 | X-RAY DIFFRACTION | 15 | C405 - 470 | | | | | | | | | | | | | | | |
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