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 | | データ収集 | HKL-3000 | | 位相決定 | SHELXS | | 位相決定 | MLPHARE | | 位相決定 | BUCCANEER | | モデル構築 | PHENIX | (phenix.refine: 1.7_650)精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | BUCCANEER | | 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→38.021 Å / SU ML: 0.5 / Isotropic thermal model: mixed / σ(F): 1.34 / 位相誤差: 17.95 / 立体化学のターゲット値: MLHL
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2022 | 1827 | 4.97 % |
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Rwork | 0.1692 | - | - |
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obs | 0.1708 | 36788 | 99.69 % |
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all | - | 36788 | - |
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溶媒の処理 | 減衰半径: 0.95 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 52.874 Å2 / ksol: 0.362 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- | 3.1442 Å2 | -0 Å2 | -0 Å2 |
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2- | - | -1.976 Å2 | 0 Å2 |
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3- | - | - | -1.1681 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2→38.021 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2999 | 0 | 84 | 283 | 3366 |
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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_d0.009 | 3240 | X-RAY DIFFRACTION | f_angle_d1.282 | 4386 | X-RAY DIFFRACTION | f_dihedral_angle_d14.09 | 1183 | X-RAY DIFFRACTION | f_chiral_restr0.11 | 502 | X-RAY DIFFRACTION | f_plane_restr0.007 | 582 | | | | | |
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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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2-2.0541 | 0.2621 | 152 | 0.2021 | 2624 | X-RAY DIFFRACTION | 99 | 2.0541-2.1145 | 0.2264 | 140 | 0.1897 | 2644 | X-RAY DIFFRACTION | 99 | 2.1145-2.1828 | 0.2103 | 119 | 0.175 | 2660 | X-RAY DIFFRACTION | 100 | 2.1828-2.2608 | 0.209 | 131 | 0.1639 | 2656 | X-RAY DIFFRACTION | 100 | 2.2608-2.3513 | 0.2064 | 135 | 0.1726 | 2660 | X-RAY DIFFRACTION | 100 | 2.3513-2.4583 | 0.1899 | 151 | 0.1747 | 2644 | X-RAY DIFFRACTION | 100 | 2.4583-2.5879 | 0.1966 | 130 | 0.1755 | 2676 | X-RAY DIFFRACTION | 100 | 2.5879-2.7499 | 0.2171 | 139 | 0.1672 | 2681 | X-RAY DIFFRACTION | 100 | 2.7499-2.9622 | 0.2095 | 145 | 0.1673 | 2684 | X-RAY DIFFRACTION | 100 | 2.9622-3.2601 | 0.1872 | 157 | 0.1574 | 2693 | X-RAY DIFFRACTION | 100 | 3.2601-3.7315 | 0.2221 | 152 | 0.1535 | 2697 | X-RAY DIFFRACTION | 100 | 3.7315-4.7 | 0.1674 | 133 | 0.1523 | 2767 | X-RAY DIFFRACTION | 100 | 4.7-38.0279 | 0.2121 | 143 | 0.1924 | 2875 | X-RAY DIFFRACTION | 100 |
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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 | 1.9043 | 0.41 | -0.4393 | 0.6986 | -0.4781 | 0.8518 | -0.065 | 0.13 | -0.1246 | -0.0286 | 0.1911 | 0.0277 | 0.053 | -0.0334 | 0.016 | 0.1905 | -0.0322 | -0.0166 | 0.1631 | 0.0372 | 0.1765 | 37.8739 | 9.0563 | 60.9806 | 2 | 1.3906 | -0.0351 | -0.9445 | 0.8175 | -0.4628 | 1.0575 | 0.0193 | -0.4308 | -0.2267 | 0.0065 | -0.0651 | -0.0598 | 0.0011 | 0.3131 | 0.025 | 0.2607 | -0.0209 | -0.0158 | 0.3317 | 0.0587 | 0.2542 | 46.5598 | 5.52 | 75.4615 | 3 | 0.4304 | -0.3547 | 0.766 | 0.7066 | -0.7818 | 1.2681 | -0.0123 | -0.0567 | -0.0412 | -0.2174 | 0.2195 | 0.2999 | 0.3683 | -0.7037 | -0.1323 | 0.2144 | -0.0737 | -0.0234 | 0.2302 | 0.081 | 0.2323 | 27.9769 | -3.7159 | 77.0421 | 4 | 2.2585 | 0.2104 | -1.0673 | 0.7449 | -0.6467 | 0.99 | 0.1949 | -0.6875 | -0.0137 | 0.2172 | -0.0307 | 0.1299 | -0.0731 | -0.0503 | -0.0757 | 0.2833 | -0.0145 | 0.0192 | 0.295 | 0.0086 | 0.2437 | 40.745 | 10.9287 | 74.6752 | 5 | 1.3331 | 0.2812 | -0.5783 | 0.8621 | -0.3161 | 2.9757 | -0.3322 | -0.0127 | -0.5178 | -0.436 | 0.4543 | 0.1679 | 0.8828 | 0.0162 | 0.0626 | 0.4716 | -0.1094 | -0.033 | 0.2691 | 0.0758 | 0.374 | 50.1861 | -2.1389 | 64.0643 | 6 | 1.1187 | -0.5 | 0.7355 | 0.3676 | -0.211 | 0.5987 | -0.2474 | -0.1265 | -0.0421 | 0.4115 | -0.0544 | -0.2705 | 0.3715 | 0.4612 | -0.3147 | 0.4539 | -0.0862 | -0.3603 | 0.5513 | 0.0509 | 0.2267 | 63.1212 | 0.8667 | 69.4335 | 7 | 0.5824 | -0.0296 | -0.7081 | 0.4061 | -0.4982 | 1.558 | -0.3082 | -0.1675 | -0.8634 | -0.5553 | 0.1886 | -0.8411 | 1.0949 | -0.0481 | 0.0744 | 0.6297 | -0.091 | -0.0468 | 0.3551 | 0.1203 | 0.4259 | 51.1729 | -4.0022 | 70.6126 | 8 | 1.5035 | -0.7075 | -0.687 | 1.3784 | -0.1406 | 0.8642 | 0.1093 | 0.1035 | 0.0392 | 0.0325 | -0.0259 | -0.1775 | -0.0696 | -0.1934 | -0.0062 | 0.1928 | -0.0153 | 0.0191 | 0.2141 | 0.0109 | 0.1979 | 53.3041 | 13.9047 | 52.0041 | 9 | 1.3731 | 0.6219 | -0.9833 | 1.0343 | -0.475 | 1.5596 | 0.0684 | 0.3373 | 0.1205 | 0.1238 | 0.078 | 0.2616 | 0.0015 | -0.3469 | -0.0842 | 0.2004 | 0.0061 | 0.0023 | 0.2868 | 0.0328 | 0.2767 | 48.0914 | 17.6715 | 47.3657 | 10 | 1.1921 | -0.0843 | -0.2919 | 0.4023 | 0.6961 | 1.8137 | -0.0008 | 0.1495 | -0.074 | 0.0756 | -0.0097 | -0.1902 | 0.3407 | -0.0146 | -0.0065 | 0.2678 | -0.0033 | -0.0051 | 0.2292 | -0.0021 | 0.257 | 62.0754 | 5.4506 | 44.6168 | 11 | 4.3645 | 1.2764 | -0.019 | 4.0886 | 1.2393 | 1.7516 | -0.3464 | -0.4142 | 0.2623 | -0.5488 | 0.0328 | 0.436 | -0.3388 | 0.2466 | 0.2124 | 0.2257 | -0.0189 | 0.0091 | 0.2442 | 0.0134 | 0.2326 | 68.9498 | 20.6207 | 31.1095 | 12 | 1.7218 | -0.0485 | -0.8241 | 0.5837 | -0.1046 | 1.3066 | 0.1692 | 0.44 | 0.4955 | -0.1619 | 0.1152 | -0.0338 | -0.1246 | -0.1555 | -0.1251 | 0.2854 | 0.0323 | 0.0311 | 0.2622 | 0.0269 | 0.3073 | 58.4246 | 22.4325 | 39.0152 | 13 | 2.3887 | 0.0746 | -0.8058 | 0.9824 | 0.2196 | 2.2264 | -0.0351 | -0.1889 | 0.2531 | 0.2172 | 0.084 | -0.0601 | 0.0483 | 0.2133 | -0.0505 | 0.2869 | 0.0048 | -0.0058 | 0.2614 | 0.0076 | 0.3159 | 61.0116 | 9.0055 | 51.2631 | 14 | 3.9262 | -2.2256 | 1.7064 | 3.7188 | 0.9033 | 2.1919 | 0.0121 | -0.2521 | -0.6758 | 0.7403 | -0.5406 | -0.7057 | 1.021 | 1.3388 | -0.1131 | 0.5242 | 0.1789 | -0.0535 | 0.587 | 0.2393 | 0.5043 | 63.6994 | -1.6545 | 60.9668 | 15 | 1.3988 | -0.4959 | -0.9094 | 1.2585 | -0.8835 | 1.9872 | 0.2343 | -0.8804 | 0.0266 | 0.1604 | -0.6109 | -0.5255 | 0.1029 | 0.6736 | 0.1033 | 0.2804 | -0.0409 | 0.0005 | 0.4616 | 0.0755 | 0.4048 | 67.6577 | 8.1383 | 55.338 |
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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 (resseq -2:77) | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 78:109)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 110:133)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 134:155)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 156:176)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 177:190)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 191:208)8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq -2:21) | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 22:77)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 78:109)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 110:124)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 125:143)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 144:173)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 174:190)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 191:208) | | | | | | | | | | | | |
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