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: 2.06→72.901 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.71 / SU ML: 0.207 / 交差検証法: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.206 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2786 | 3626 | 5.067 % |
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Rwork | 0.2448 | 67938 | - |
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all | 0.246 | - | - |
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obs | - | 71564 | 99.695 % |
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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: 49.091 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.909 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 1.909 Å2 | 0 Å2 |
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3- | - | - | -3.818 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.06→72.901 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8019 | 0 | 86 | 325 | 8430 |
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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_d0.004 | 0.013 | 8270 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.014 | 7772 | X-RAY DIFFRACTION | r_angle_refined_deg1.306 | 1.646 | 11247 | X-RAY DIFFRACTION | r_angle_other_deg1.125 | 1.579 | 17865 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.832 | 5 | 1038 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg32.526 | 21.204 | 432 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.597 | 15 | 1379 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.164 | 15 | 71 | X-RAY DIFFRACTION | r_chiral_restr0.047 | 0.2 | 1143 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 9351 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1911 | X-RAY DIFFRACTION | r_nbd_refined0.176 | 0.2 | 1409 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.174 | 0.2 | 7744 | X-RAY DIFFRACTION | r_nbtor_refined0.145 | 0.2 | 3896 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.069 | 0.2 | 4044 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.134 | 0.2 | 440 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.044 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.038 | 0.2 | 4 | X-RAY DIFFRACTION | r_nbd_other0.162 | 0.2 | 30 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.118 | 0.2 | 5 | X-RAY DIFFRACTION | r_mcbond_it0.989 | 3.363 | 4155 | X-RAY DIFFRACTION | r_mcbond_other0.989 | 3.363 | 4154 | X-RAY DIFFRACTION | r_mcangle_it1.546 | 5.041 | 5192 | X-RAY DIFFRACTION | r_mcangle_other1.545 | 5.042 | 5193 | X-RAY DIFFRACTION | r_scbond_it1.115 | 3.552 | 4115 | X-RAY DIFFRACTION | r_scbond_other1.115 | 3.553 | 4116 | X-RAY DIFFRACTION | r_scangle_it1.81 | 5.286 | 6055 | X-RAY DIFFRACTION | r_scangle_other1.809 | 5.287 | 6056 | X-RAY DIFFRACTION | r_lrange_it5.618 | 39.989 | 8837 | X-RAY DIFFRACTION | r_lrange_other5.562 | 39.825 | 8795 | X-RAY DIFFRACTION | r_ncsr_local_group_10.083 | 0.05 | 16750 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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 ncs0.08339 | 0.0501 | 1 | 2 | BX-RAY DIFFRACTION | Local ncs0.08339 | 0.0501 | | | | |
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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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2.06-2.113 | 0.382 | 247 | 0.361 | 4935 | X-RAY DIFFRACTION | 99.9614 | 2.113-2.171 | 0.364 | 257 | 0.339 | 4839 | X-RAY DIFFRACTION | 100 | 2.171-2.234 | 0.391 | 242 | 0.341 | 4629 | X-RAY DIFFRACTION | 98.7632 | 2.234-2.303 | 0.623 | 247 | 0.56 | 4417 | X-RAY DIFFRACTION | 97.106 | 2.303-2.378 | 0.317 | 235 | 0.295 | 4407 | X-RAY DIFFRACTION | 100 | 2.378-2.462 | 0.302 | 236 | 0.274 | 4307 | X-RAY DIFFRACTION | 99.934 | 2.462-2.555 | 0.34 | 195 | 0.259 | 4171 | X-RAY DIFFRACTION | 100 | 2.555-2.659 | 0.332 | 204 | 0.27 | 4007 | X-RAY DIFFRACTION | 100 | 2.659-2.777 | 0.326 | 218 | 0.261 | 3846 | X-RAY DIFFRACTION | 99.9754 | 2.777-2.913 | 0.317 | 231 | 0.259 | 3644 | X-RAY DIFFRACTION | 100 | 2.913-3.071 | 0.256 | 187 | 0.242 | 3540 | X-RAY DIFFRACTION | 100 | 3.071-3.257 | 0.293 | 179 | 0.247 | 3312 | X-RAY DIFFRACTION | 100 | 3.257-3.482 | 0.275 | 189 | 0.241 | 3145 | X-RAY DIFFRACTION | 100 | 3.482-3.761 | 0.268 | 149 | 0.251 | 2935 | X-RAY DIFFRACTION | 99.7735 | 3.761-4.119 | 0.259 | 143 | 0.213 | 2724 | X-RAY DIFFRACTION | 100 | 4.119-4.606 | 0.197 | 123 | 0.186 | 2498 | X-RAY DIFFRACTION | 100 | 4.606-5.318 | 0.209 | 134 | 0.184 | 2219 | X-RAY DIFFRACTION | 100 | 5.318-6.513 | 0.261 | 90 | 0.189 | 1910 | X-RAY DIFFRACTION | 100 | 6.513-9.209 | 0.191 | 79 | 0.183 | 1522 | X-RAY DIFFRACTION | 100 | 9.209-72.901 | 0.208 | 41 | 0.212 | 932 | X-RAY DIFFRACTION | 99.3871 |
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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 | 0.8746 | -0.2521 | -0.0629 | 1.1425 | 0.5759 | 1.0802 | -0.0484 | -0.1885 | 0.1301 | 0.1406 | -0.0084 | 0.0495 | -0.0022 | 0.1471 | 0.0568 | 0.0279 | -0.0233 | -0.0009 | 0.1545 | -0.0464 | 0.0422 | 0.754 | 15.8953 | 34.2647 | 2 | 1.0304 | -0.0024 | -0.2508 | 0.9564 | 0.2651 | 0.6407 | 0.0306 | -0.1146 | -0.0982 | 0.0354 | -0.0568 | -0.1718 | 0.2523 | 0.2919 | 0.0262 | 0.1335 | 0.1375 | 0.0009 | 0.2457 | 0.0961 | 0.109 | 19.1637 | -17.0486 | 13.2945 |
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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 | 2 | ALLB34 - 552 | | | | |
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