ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0005精密化 | HKL-2000 | | データ削減 | SCALEPACK | | データスケーリング | SnB | | 位相決定 | SOLVE | | 位相決定 | 直接法 | | 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: 1.85→48.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.292 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 2 / ESU R: 0.149 / ESU R Free: 0.141 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.22829 | 2197 | 5.1 % | RANDOM |
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Rwork | 0.18344 | - | - | - |
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obs | 0.18577 | 41282 | 98.7 % | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 33.804 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.42 Å2 | 0 Å2 | -0.55 Å2 |
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2- | - | 1.32 Å2 | 0 Å2 |
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3- | - | - | -0.99 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.85→48.1 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3792 | 0 | 0 | 392 | 4184 |
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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_d0.014 | 0.022 | 4083 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.127 | 1.977 | 5521 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg4.086 | 5 | 544 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.685 | 24.894 | 188 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.279 | 15 | 876 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.493 | 15 | 31 | X-RAY DIFFRACTION | r_chiral_restr0.082 | 0.2 | 624 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 3001 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.225 | 0.3 | 2092 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.312 | 0.5 | 2877 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.271 | 0.5 | 541 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.216 | 0.3 | 42 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.233 | 0.5 | 37 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it2.27 | 2 | 2584 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it3.014 | 3 | 4067 | X-RAY DIFFRACTION | r_scbond_it3.108 | 2 | 1650 | X-RAY DIFFRACTION | r_scangle_it4.514 | 3 | 1415 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.85→1.898 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.335 | 155 | - |
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Rwork | 0.249 | 2619 | - |
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obs | - | 2774 | 86.69 % |
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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 | 10.4014 | 6.1543 | 9.4076 | 22.238 | 10.1675 | 27.2535 | -2.3338 | 2.3244 | -0.4015 | -1.2947 | -0.5783 | -0.1325 | 0.7767 | -0.1245 | 2.9121 | 0.2408 | -0.0584 | 0.621 | 0.5907 | -0.113 | 0.2568 | 2.121 | 6.162 | -7.779 | 2 | 3.9279 | -0.5006 | 4.0067 | 0.1115 | -1.0667 | 10.5675 | 0.0111 | 0.9321 | 0.1331 | -0.1267 | -0.0918 | -0.0976 | 0.0392 | 0.455 | 0.0807 | -0.0241 | -0.0014 | 0.0018 | 0.4064 | -0.0108 | -0.1949 | 13.799 | 6.977 | 14.806 | 3 | 1.225 | 0.659 | 0.9609 | 0.4616 | 0.6702 | 2.6716 | 0.05 | 0.1782 | -0.005 | 0.0754 | -0.0344 | -0.025 | 0.0505 | -0.0377 | -0.0156 | -0.0599 | 0.009 | 0 | -0.0268 | -0.0257 | -0.0307 | 23.926 | 6.441 | 44.016 | 4 | 0.9477 | -0.0464 | 0.4328 | 0.3253 | 0.5474 | 1.5076 | 0.016 | -0.0488 | 0.027 | -0.036 | 0.0042 | -0.0062 | -0.02 | -0.0878 | -0.0201 | -0.0476 | -0.0095 | 0.0082 | -0.0728 | 0.0048 | -0.011 | 33.683 | 18.419 | 73.275 | 5 | 9.7938 | 0.8595 | 1.4688 | 0.7687 | 1.7986 | 5.3449 | 0.1022 | -0.6066 | 1.1393 | -0.2078 | 0.0796 | 0.1792 | -0.5445 | 0.3758 | -0.1818 | 0.0314 | -0.0743 | 0.0453 | 0.1095 | -0.1635 | 0.0572 | 45.328 | 29.313 | 92.483 | 6 | 27.8026 | -4.3742 | -5.4719 | 74.3715 | -26.9526 | 89.4629 | -0.7001 | -0.4398 | -1.3305 | -1.5686 | -0.5108 | -0.8431 | 0.3081 | 2.6525 | 1.2109 | 0.2691 | -0.0307 | -0.0134 | 0.3254 | -0.0761 | 0.3882 | 64.39 | 25.361 | 134.473 | 7 | 4.2518 | 1.3581 | -1.4103 | 3.6204 | -2.0379 | 9.1532 | 0.4161 | -1.7196 | 0.2019 | 0.8762 | -0.5551 | -0.0921 | -0.7801 | 1.1299 | 0.139 | 0.1426 | -0.3017 | -0.0417 | 0.8078 | -0.0876 | -0.1527 | 57.639 | 22.009 | 112.977 | 8 | 1.3667 | 0.3301 | -0.1236 | 0.0801 | -0.0076 | 1.2792 | 0.0811 | -0.2603 | -0.0919 | -0.023 | -0.0321 | -0.0008 | 0.0654 | 0.1571 | -0.0491 | -0.0356 | -0.0046 | -0.0226 | -0.015 | 0.0115 | 0.0261 | 49.941 | 15.909 | 83.852 | 9 | 1.0549 | 0.3245 | 1.1641 | 0.3888 | 0.4908 | 1.7078 | 0.0212 | 0.1659 | 0.0627 | -0.0437 | -0.0065 | -0.0833 | -0.1153 | 0.1135 | -0.0147 | -0.0439 | 0.0035 | 0.0182 | -0.0499 | 0.017 | 0.001 | 36.713 | 17.535 | 53.762 | 10 | 8.0074 | 1.241 | 1.9562 | 2.9122 | 3.1753 | 5.5614 | -0.0371 | 0.4125 | 0.4589 | -0.6898 | -0.1992 | 0.2746 | -0.9238 | 0.0812 | 0.2363 | 0.0658 | 0.0863 | -0.0611 | -0.0059 | 0.0746 | -0.0545 | 22.448 | 18.631 | 35.148 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA142 - 172 | 145 - 175 | 2 | X-RAY DIFFRACTION | 2 | AA-2 - 18 | 1 - 21 | 3 | X-RAY DIFFRACTION | 2 | AA173 - 191 | 176 - 194 | 4 | X-RAY DIFFRACTION | 2 | AA122 - 141 | 125 - 144 | 5 | X-RAY DIFFRACTION | 3 | AA19 - 41 | 22 - 44 | 6 | X-RAY DIFFRACTION | 3 | AA100 - 121 | 103 - 124 | 7 | X-RAY DIFFRACTION | 3 | AA192 - 211 | 195 - 214 | 8 | X-RAY DIFFRACTION | 4 | AA42 - 64 | 45 - 67 | 9 | X-RAY DIFFRACTION | 4 | AA76 - 99 | 79 - 102 | 10 | X-RAY DIFFRACTION | 4 | AA212 - 232 | 215 - 235 | 11 | X-RAY DIFFRACTION | 5 | AA233 - 246 | 236 - 249 | 12 | X-RAY DIFFRACTION | 5 | AA65 - 75 | 68 - 78 | 13 | X-RAY DIFFRACTION | 6 | BB142 - 172 | 145 - 175 | 14 | X-RAY DIFFRACTION | 7 | BB-2 - 18 | 1 - 21 | 15 | X-RAY DIFFRACTION | 7 | BB173 - 191 | 176 - 194 | 16 | X-RAY DIFFRACTION | 7 | BB122 - 141 | 125 - 144 | 17 | X-RAY DIFFRACTION | 8 | BB19 - 41 | 22 - 44 | 18 | X-RAY DIFFRACTION | 8 | BB100 - 121 | 103 - 124 | 19 | X-RAY DIFFRACTION | 8 | BB192 - 211 | 195 - 214 | 20 | X-RAY DIFFRACTION | 9 | BB42 - 64 | 45 - 67 | 21 | X-RAY DIFFRACTION | 9 | BB76 - 99 | 79 - 102 | 22 | X-RAY DIFFRACTION | 9 | BB212 - 232 | 215 - 235 | 23 | X-RAY DIFFRACTION | 10 | BB233 - 242 | 236 - 245 | 24 | X-RAY DIFFRACTION | 10 | BB65 - 75 | 68 - 78 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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