ソフトウェア | 名称 | バージョン | 分類 |
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ADSC | Quantumデータ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.6.4_486)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: 分子置換 開始モデル: 1F3H 解像度: 2.6→29.272 Å / SU ML: 0.46 / σ(F): 1.34 / σ(I): 0 / 位相誤差: 33.46 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2734 | 811 | 5.11 % | RANDOM |
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Rwork | 0.2217 | - | - | - |
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obs | 0.2247 | 15872 | 98.87 % | - |
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all | - | 16683 | - | - |
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溶媒の処理 | 減衰半径: 1.17 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 67.224 Å2 / ksol: 0.306 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 4.8234 Å2 | 0 Å2 | 16.1418 Å2 |
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2- | - | -10.3216 Å2 | 0 Å2 |
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3- | - | - | 5.4982 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.6→29.272 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2274 | 0 | 2 | 17 | 2293 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.013 | 2330 | X-RAY DIFFRACTION | f_angle_d1.43 | 3128 | X-RAY DIFFRACTION | f_dihedral_angle_d20.448 | 898 | X-RAY DIFFRACTION | f_chiral_restr0.099 | 320 | X-RAY DIFFRACTION | f_plane_restr0.008 | 410 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.6001-2.7629 | 0.3956 | 136 | 0.3309 | 2462 | X-RAY DIFFRACTION | 98 | 2.7629-2.976 | 0.3201 | 134 | 0.2773 | 2510 | X-RAY DIFFRACTION | 100 | 2.976-3.2752 | 0.3305 | 133 | 0.2443 | 2522 | X-RAY DIFFRACTION | 100 | 3.2752-3.7482 | 0.2816 | 111 | 0.2315 | 2562 | X-RAY DIFFRACTION | 100 | 3.7482-4.7192 | 0.2306 | 155 | 0.1921 | 2499 | X-RAY DIFFRACTION | 99 | 4.7192-29.2737 | 0.2718 | 142 | 0.2115 | 2506 | X-RAY DIFFRACTION | 97 |
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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 | 1.3994 | -0.5412 | -1.6367 | 0.2491 | 1.0739 | 4.2789 | 0.5555 | -1.7505 | 5.576 | -0.0751 | 1.6271 | -0.7593 | -1.8561 | -0.4499 | -0.0614 | 0.4325 | 0.2532 | -0.315 | 1.0803 | -0.5315 | 1.8084 | 16.5534 | 5.6231 | 14.785 | 2 | 1.053 | 0.4895 | -1.1101 | 4.9565 | -2.2106 | 1.1798 | -0.1346 | -0.2546 | -0.356 | 0.4262 | 0.2709 | 0.3435 | 0.6104 | -0.0415 | -0.121 | 0.5551 | 0.0109 | -0.0225 | 0.4781 | -0.0611 | 0.2937 | 24.3987 | -10.7102 | 11.0289 | 3 | 0.4153 | 0.1686 | 0.7223 | 0.416 | 0.3296 | 1.1572 | -0.6971 | 2.6234 | -0.4378 | 0.0085 | 1.2732 | 2.2866 | -1.787 | 0.0098 | -0.0664 | 1.2642 | -0.2084 | -0.3114 | 1.201 | -0.1609 | 0.7997 | 21.309 | -10.8228 | -4.5527 | 4 | 4.4025 | 2.0209 | -1.329 | 2.0686 | 0.0335 | 1.5246 | 0.0032 | 0.5139 | -0.2323 | -1.1334 | -0.054 | -0.7769 | 0.0233 | 0.0532 | -0.1243 | 0.7071 | 0.1014 | -0.0801 | 0.4598 | -0.175 | 0.3931 | 30.7832 | -8.3301 | 4.0248 | 5 | 2.7023 | -0.7367 | 0.6056 | 0.9914 | -0.6679 | 0.2596 | -0.2988 | -0.3344 | 0.3264 | -0.0814 | 0.6498 | -0.9926 | -0.1715 | 1.0655 | -0.0075 | 0.6249 | 0.0638 | -0.0304 | 0.8264 | -0.1607 | 0.7336 | 37.3842 | -3.0944 | 9.3567 | 6 | 1.4745 | -1.2139 | -0.6548 | 1.1103 | 0.346 | 0.3336 | -2.4621 | -1.1841 | -2.9608 | 0.759 | 0.6997 | 1.2886 | 1.0919 | -0.1889 | -0.0266 | 0.9309 | 0.3543 | -0.0736 | 1.2141 | 0.0586 | 1.1534 | 28.6131 | 1.9319 | 23.6905 | 7 | 0.4945 | -0.1401 | -0.5055 | -3.583 | -0.4327 | 5.2389 | 0.0367 | 0.0467 | 0.3539 | -0.2074 | 0.1802 | -0.1931 | -0.1977 | -0.2174 | -0.033 | 0.9896 | 0.0332 | 0.0402 | 0.3483 | -0.0578 | 0.5422 | 29.1322 | 7.8047 | -1.0395 | 8 | 6.8132 | 0.1948 | -1.9643 | 0.3528 | 0.6458 | 3.1632 | 0.6597 | -0.0605 | -1.3349 | 0.7511 | -1.1328 | -0.2865 | 2.2618 | 0.9306 | -0.0239 | 0.707 | 0.0793 | 0.068 | 0.9628 | 0.0564 | 0.6902 | 31.2178 | 2.8101 | -31.8815 | 9 | 0.2352 | -0.2798 | 0.0537 | 0.6356 | -0.0329 | -0.0179 | -0.0669 | 0.3313 | -1.9422 | 2.6412 | 1.0425 | -1.9872 | 2.6177 | -0.3641 | -0.067 | 1.1742 | 0.175 | -0.3857 | 1.0435 | -0.0148 | 0.6288 | 15.7089 | 14.2176 | 16.3293 | 10 | 1.383 | 1.0034 | 1.2698 | 4.2041 | 1.1908 | 0.6411 | 0.3183 | 0.5489 | -0.1295 | -1.6944 | -0.7351 | -0.4538 | -0.2263 | 0.6688 | -0.0589 | 0.8416 | 0.0842 | 0.1121 | 0.6291 | 0.0117 | 0.7836 | 15.9561 | 23.018 | 22.6671 | 11 | 0.071 | 0.2131 | -0.1652 | 0.7819 | 0.7124 | 1.673 | 1.4714 | 0.5814 | -0.5679 | -0.4462 | 0.3724 | 0.3672 | -0.4606 | 0.941 | -0.1692 | 0.7329 | 0.0856 | -0.1672 | 0.7072 | -0.132 | 1.735 | 10.6347 | 36.4841 | 26.4282 | 12 | 1.2483 | 1.3308 | 0.6218 | 1.724 | 0.8511 | 1.1301 | -1.4297 | -0.5256 | 1.3156 | 0.8605 | 1.5731 | -0.1525 | -0.0748 | 0.6048 | -0.0674 | 0.5445 | 0.0437 | 0.0835 | 0.5289 | -0.2155 | 1.1875 | 15.5348 | 30.933 | 31.7408 | 13 | 0.2985 | -0.2508 | -0.5041 | -0.2119 | -0.0763 | 0.3977 | 0.1852 | -0.8517 | 0.2101 | 1.7087 | -0.1412 | 3.1291 | -0.9618 | 0.7836 | -0.028 | 0.75 | 0.1462 | -0.2675 | 0.6359 | -0.272 | 1.5291 | 1.0962 | 30.6874 | 26.341 | 14 | 3.4642 | 0.643 | 1.179 | 2.5631 | -0.6308 | 2.967 | -0.0431 | -0.6845 | 0.5043 | 0.6283 | -0.0105 | 1.2917 | 0.0576 | -0.59 | -0.034 | 0.4296 | 0.1229 | 0.1331 | 0.5731 | -0.1955 | 0.8721 | 9.745 | 24.2814 | 36.3049 | 15 | 4.6149 | -2.1283 | 1.5715 | 1.7658 | 1.9801 | 4.4802 | -0.5752 | -1.2083 | -1.2303 | 0.5448 | 0.1036 | 0.1948 | 0.7219 | 0.2247 | -0.0428 | 0.6283 | 0.0817 | -0.0834 | 0.6716 | -0.1516 | 0.8395 | 20.5988 | 11.2484 | 28.6365 | 16 | 3.3972 | 0.6649 | 1.6783 | 0.3111 | -0.8935 | -1.2312 | -0.0594 | -0.5182 | 0.6832 | 0.1059 | 0.1635 | -0.764 | -0.1269 | -0.1227 | -0.0289 | 0.7166 | -0.0629 | 0.1991 | 0.5882 | -0.0789 | 0.7168 | -13.3589 | 12.4073 | 34.3928 |
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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 | (chain A and resid 5:10)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 11:45)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 46:52)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 53:74)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 75:90)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 91:96)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 97:131)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 132:139)9 | X-RAY DIFFRACTION | 9 | (chain B and resid 5:10)10 | X-RAY DIFFRACTION | 10 | (chain B and resid 11:21)11 | X-RAY DIFFRACTION | 11 | (chain B and resid 22:29)12 | X-RAY DIFFRACTION | 12 | (chain B and resid 30:43)13 | X-RAY DIFFRACTION | 13 | (chain B and resid 44:54)14 | X-RAY DIFFRACTION | 14 | (chain B and resid 55:88)15 | X-RAY DIFFRACTION | 15 | (chain B and resid 89:108)16 | X-RAY DIFFRACTION | 16 | (chain B and resid 109:139) | | | | | | | | | | | | | | | |
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