ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.10.1_2155精密化 | HKL-2000 | | データ削減 | HKL-2000 | | 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: 分子置換 開始モデル: 1JC5 解像度: 1.997→44.659 Å / SU ML: 0.22 / 交差検証法: FREE R-VALUE / σ(F): 1.4 / 位相誤差: 27.01 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2334 | 817 | 4.92 % |
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Rwork | 0.1868 | - | - |
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obs | 0.1891 | 16612 | 99.42 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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精密化ステップ | サイクル: LAST / 解像度: 1.997→44.659 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2267 | 0 | 5 | 53 | 2325 |
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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_d0.008 | 2303 | X-RAY DIFFRACTION | f_angle_d0.897 | 3127 | X-RAY DIFFRACTION | f_dihedral_angle_d18.746 | 1399 | X-RAY DIFFRACTION | f_chiral_restr0.058 | 370 | X-RAY DIFFRACTION | f_plane_restr0.005 | 409 | | | | | |
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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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1.9967-2.1218 | 0.2693 | 143 | 0.1992 | 2597 | X-RAY DIFFRACTION | 99 | 2.1218-2.2856 | 0.2492 | 152 | 0.1955 | 2594 | X-RAY DIFFRACTION | 100 | 2.2856-2.5156 | 0.285 | 115 | 0.2072 | 2653 | X-RAY DIFFRACTION | 100 | 2.5156-2.8795 | 0.2937 | 123 | 0.2195 | 2662 | X-RAY DIFFRACTION | 100 | 2.8795-3.6277 | 0.2436 | 134 | 0.1942 | 2656 | X-RAY DIFFRACTION | 100 | 3.6277-44.6697 | 0.1887 | 150 | 0.1613 | 2633 | X-RAY DIFFRACTION | 98 |
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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 | 5.9828 | -0.1182 | -0.817 | 6.2416 | -1.593 | 4.8571 | -0.3951 | -1.0298 | 0.0455 | 0.2073 | 0.8253 | 0.0501 | 0.2986 | 0.1685 | -0.3041 | 0.4176 | 0.0207 | -0.0439 | 0.5198 | -0.1258 | 0.3728 | 2.5019 | -14.8044 | 3.7547 | 2 | 2.9829 | -0.1284 | -0.1172 | 5.4928 | 3.3613 | 5.5447 | -0.0306 | -0.1379 | -0.3114 | 0.4423 | -0.0412 | -0.1259 | 0.4337 | 0.2334 | 0.0989 | 0.2359 | 0.0318 | -0.0205 | 0.1797 | 0.0425 | 0.2595 | 14.122 | 0.0694 | 11.5892 | 3 | 4.0577 | 0.0113 | -1.01 | 3.0675 | -0.2035 | 3.4521 | -0.1683 | -0.2262 | -0.1972 | -0.233 | 0.0807 | -0.2798 | 0.304 | 0.8207 | 0.0571 | 0.3071 | 0.0673 | -0.017 | 0.3786 | 0.0094 | 0.2907 | 20.9532 | -0.2556 | 17.7901 | 4 | 3.1527 | 0.3702 | -0.8301 | 2.9634 | -0.6909 | 3.8311 | -0.0701 | 0.4457 | 1.0127 | -0.7529 | 0.3421 | 0.0708 | -0.5214 | 0.3092 | -0.2592 | 0.3541 | -0.1112 | 0.0223 | 0.3034 | 0.0578 | 0.428 | 18.6228 | 11.2064 | 11.3669 | 5 | 3.8529 | -0.5163 | -0.4008 | 1.6287 | 0.6099 | 4.2668 | -0.0851 | 0.8914 | -0.2628 | -0.2265 | 0.5186 | -0.1832 | 0.0431 | 0.4583 | -0.2619 | 0.2328 | -0.08 | 0.0193 | 0.354 | -0.0489 | 0.2518 | 11.1448 | -1.4774 | -0.3564 | 6 | 4.7466 | 0.3199 | -0.2095 | 4.6486 | -0.6591 | 5.4521 | 0.0332 | 1.0046 | 0.2865 | -0.3392 | 0.0503 | -0.2802 | -0.2056 | 0.4578 | -0.1246 | 0.2269 | -0.0296 | 0.007 | 0.3535 | -0.013 | 0.2235 | 14.0897 | 3.4068 | -2.3818 | 7 | 0.022 | -0.1551 | 0.07 | 0.5961 | -0.67 | 1.0062 | -0.1188 | 0.1351 | -0.3926 | 0.0176 | -0.0624 | -0.3332 | 0.4706 | 0.3078 | 0.1164 | 0.3239 | 0.1292 | -0.012 | 0.3767 | -0.0687 | 0.4651 | 21.1641 | -7.8425 | 1.2755 | 8 | 6.7174 | -0.5905 | -1.2881 | 6.3804 | 2.6189 | 6.0887 | -0.0034 | 0.8819 | -0.0692 | 0.0484 | 0.402 | 0.195 | -0.0104 | -0.0011 | -0.3879 | 0.4065 | 0.0417 | -0.1082 | 0.4417 | 0.1331 | 0.3747 | 14.7639 | -14.159 | 21.6959 | 9 | 1.8582 | -0.6457 | 1.2849 | 3.9318 | -2.4142 | 3.3662 | -0.0241 | 0.0468 | -0.1413 | -0.0839 | -0.1885 | 0.0734 | 0.2301 | -0.0547 | 0.1133 | 0.2645 | 0.0035 | 0.0273 | 0.1364 | 0.0103 | 0.2907 | 1.9515 | -0.3429 | 14.0538 | 10 | 4.2495 | -0.6798 | -0.8479 | 3.1846 | 0.161 | 2.1087 | -0.056 | 0.778 | -0.1476 | -0.2594 | 0.1499 | 0.6287 | 0.1316 | -0.4883 | -0.0462 | 0.2552 | -0.0419 | -0.0645 | 0.3629 | 0.0081 | 0.3583 | -5.0961 | -1.2956 | 4.487 | 11 | 3.5406 | -2.9827 | -1.2117 | 7.0221 | 1.2603 | 4.3104 | -0.1603 | 0.0753 | 0.0077 | 0.8794 | -0.0818 | 0.5799 | 0.1238 | -0.5573 | 0.2632 | 0.3768 | -0.0797 | 0.085 | 0.2868 | -0.0401 | 0.4469 | -4.5091 | -1.6345 | 13.0928 | 12 | 3.5508 | 2.1819 | 0.17 | 1.5923 | -0.872 | 3.6995 | -0.145 | -0.3437 | 0.5292 | 0.462 | 0.3646 | 0.7121 | -0.1552 | -0.6922 | -0.2549 | 0.2862 | 0.0622 | 0.0561 | 0.2788 | 0.0066 | 0.3883 | -5.8823 | 6.7232 | 13.8183 | 13 | 5.2196 | -3.1961 | 1.5707 | 4.0478 | -2.4833 | 3.2753 | 0.0364 | -0.1925 | 0.3021 | 0.1673 | 0.1229 | 0.3152 | -0.6217 | -0.5916 | 0.016 | 0.3331 | 0.0522 | 0.0112 | 0.2641 | -0.0013 | 0.308 | 1.6002 | 8.0076 | 15.5845 | 14 | 3.9787 | 0.0965 | -0.0391 | 2.9697 | -0.1523 | 3.7291 | 0.0135 | -0.9105 | -0.0892 | 0.5682 | 0.0719 | 0.3184 | 0.1469 | -0.4703 | 0.0231 | 0.3538 | 0.0589 | 0.0501 | 0.4316 | 0.0512 | 0.2238 | 2.7518 | 1.1545 | 29.578 | 15 | 5.4333 | 4.2195 | -0.804 | 3.2074 | -0.5776 | 0.1418 | -0.2003 | -0.0819 | -0.5256 | -0.1609 | -0.0029 | -0.1044 | 0.5257 | -0.1869 | 0.3177 | 0.414 | -0.1052 | 0.0619 | 0.3164 | 0.0083 | 0.3799 | -5.5469 | -8.5879 | 24.8028 |
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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 8 through 17 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 18 through 30 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 31 through 69 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 70 through 90 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 91 through 113 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 114 through 144 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 145 through 157 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 8 through 17 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 18 through 30 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 31 through 52 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 53 through 69 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 70 through 81 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 82 through 101 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 102 through 144 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 145 through 158 ) | | | | | | | | | | | | | | |
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