ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0267精密化 | xia2 | | データ削減 | Aimless | | 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: 4bbw 解像度: 1.659→78.005 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.357 / SU ML: 0.131 / 交差検証法: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.122 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2727 | 6556 | 4.917 % |
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Rwork | 0.2218 | 126770 | - |
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all | 0.224 | - | - |
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obs | - | 133326 | 98.77 % |
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溶媒の処理 | イオンプローブ半径: 0.9 Å / 減衰半径: 0.9 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT |
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原子変位パラメータ | Biso mean: 29.929 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.764 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.764 Å2 | 0 Å2 |
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3- | - | - | -1.529 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.659→78.005 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8046 | 0 | 40 | 704 | 8790 |
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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 | 0.013 | 8268 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.014 | 7842 | X-RAY DIFFRACTION | r_angle_refined_deg1.681 | 1.645 | 11214 | X-RAY DIFFRACTION | r_angle_other_deg1.357 | 1.58 | 18012 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg8.163 | 5 | 1044 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.129 | 21.284 | 436 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.289 | 15 | 1404 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.714 | 15 | 72 | X-RAY DIFFRACTION | r_chiral_restr0.079 | 0.2 | 1118 | X-RAY DIFFRACTION | r_gen_planes_refined0.009 | 0.02 | 9388 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1920 | X-RAY DIFFRACTION | r_nbd_refined0.198 | 0.2 | 1447 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.188 | 0.2 | 7931 | X-RAY DIFFRACTION | r_nbtor_refined0.155 | 0.2 | 3918 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.078 | 0.2 | 4146 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.155 | 0.2 | 679 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.105 | 0.2 | 2 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.178 | 0.2 | 5 | X-RAY DIFFRACTION | r_nbd_other0.176 | 0.2 | 20 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.126 | 0.2 | 5 | X-RAY DIFFRACTION | r_mcbond_it7.106 | 1.728 | 4170 | X-RAY DIFFRACTION | r_mcbond_other7.106 | 1.728 | 4169 | X-RAY DIFFRACTION | r_mcangle_it6.747 | 2.562 | 5216 | X-RAY DIFFRACTION | r_mcangle_other6.747 | 2.562 | 5217 | X-RAY DIFFRACTION | r_scbond_it10.58 | 2.083 | 4098 | X-RAY DIFFRACTION | r_scbond_other10.579 | 2.083 | 4099 | X-RAY DIFFRACTION | r_scangle_it10.725 | 2.946 | 5998 | X-RAY DIFFRACTION | r_scangle_other10.725 | 2.947 | 5999 | X-RAY DIFFRACTION | r_lrange_it11.082 | 21.806 | 9115 | X-RAY DIFFRACTION | r_lrange_other11.131 | 21.286 | 8950 | X-RAY DIFFRACTION | r_ncsr_local_group_10.089 | 0.05 | 16907 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Refine-ID | タイプ | Rms dev position (Å) | Weight position |
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1 | 1 | AX-RAY DIFFRACTION | Local ncs0.0889 | 0.05009 | 1 | 2 | BX-RAY DIFFRACTION | Local ncs0.0889 | 0.05009 | | | | |
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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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1.659-1.702 | 0.404 | 473 | 0.396 | 9300 | X-RAY DIFFRACTION | 99.3999 | 1.702-1.749 | 0.377 | 465 | 0.361 | 9076 | X-RAY DIFFRACTION | 99.979 | 1.749-1.8 | 0.337 | 461 | 0.328 | 8870 | X-RAY DIFFRACTION | 99.8929 | 1.8-1.855 | 0.333 | 450 | 0.31 | 8633 | X-RAY DIFFRACTION | 99.8571 | 1.855-1.916 | 0.369 | 442 | 0.305 | 8302 | X-RAY DIFFRACTION | 99.5333 | 1.916-1.983 | 0.318 | 364 | 0.278 | 8121 | X-RAY DIFFRACTION | 99.5425 | 1.983-2.058 | 0.304 | 414 | 0.246 | 7784 | X-RAY DIFFRACTION | 99.4541 | 2.058-2.142 | 0.303 | 381 | 0.239 | 7488 | X-RAY DIFFRACTION | 99.3937 | 2.142-2.237 | 0.288 | 365 | 0.238 | 7170 | X-RAY DIFFRACTION | 98.8586 | 2.237-2.346 | 0.319 | 346 | 0.237 | 6897 | X-RAY DIFFRACTION | 98.6785 | 2.346-2.473 | 0.281 | 343 | 0.214 | 6478 | X-RAY DIFFRACTION | 98.4413 | 2.473-2.623 | 0.308 | 321 | 0.214 | 6152 | X-RAY DIFFRACTION | 97.7499 | 2.623-2.804 | 0.303 | 312 | 0.226 | 5746 | X-RAY DIFFRACTION | 97.3329 | 2.804-3.029 | 0.262 | 278 | 0.216 | 5365 | X-RAY DIFFRACTION | 96.7759 | 3.029-3.318 | 0.257 | 264 | 0.209 | 4964 | X-RAY DIFFRACTION | 96.618 | 3.318-3.71 | 0.273 | 251 | 0.216 | 4475 | X-RAY DIFFRACTION | 97.063 | 3.71-4.284 | 0.218 | 187 | 0.178 | 4074 | X-RAY DIFFRACTION | 97.5504 | 4.284-5.246 | 0.181 | 203 | 0.143 | 3473 | X-RAY DIFFRACTION | 98.0267 | 5.246-7.418 | 0.181 | 143 | 0.151 | 2752 | X-RAY DIFFRACTION | 97.5076 | 7.418-78.005 | 0.266 | 93 | 0.187 | 1650 | X-RAY DIFFRACTION | 98.4746 |
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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 | 0.8082 | -0.1349 | 0.0614 | 0.9628 | 0.2673 | 0.5405 | -0.0217 | -0.0949 | 0.0757 | 0.1145 | 0.0028 | 0.0339 | -0.0068 | 0.0246 | 0.0189 | 0.0334 | -0.0048 | 0.0028 | 0.0977 | -0.0277 | 0.0134 | 0.8541 | 16.0017 | 34.2084 | 2 | 0.9901 | 0.1325 | -0.2589 | 0.9128 | 0.1225 | 0.5725 | 0.0091 | -0.0253 | -0.0966 | -0.0163 | -0.0137 | -0.1255 | 0.1398 | 0.0809 | 0.0046 | 0.0919 | 0.0811 | 0.0038 | 0.1009 | 0.0243 | 0.0405 | 19.0152 | -17.121 | 13.3773 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA34 - 552 | 2 | X-RAY DIFFRACTION | 1 | ALLA601 | 3 | X-RAY DIFFRACTION | 1 | ALLA701 | 4 | X-RAY DIFFRACTION | 1 | ALLA801 | 5 | X-RAY DIFFRACTION | 1 | ALLA901 | 6 | X-RAY DIFFRACTION | 2 | ALLB34 - 552 | 7 | X-RAY DIFFRACTION | 2 | ALLB601 | 8 | X-RAY DIFFRACTION | 2 | ALLB701 | | | | | | | | | | | | | | | | |
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