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 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | BALBES | | 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: 2FJY 解像度: 1.3→20.866 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0.05 / SU B: 2.525 / SU ML: 0.046 / Data cutoff high absF: 2 / Data cutoff low absF: 2 / 交差検証法: THROUGHOUT / σ(F): 2 / ESU R: 0.08 / ESU R Free: 0.064 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1976 | 1108 | 4.961 % | RANDOM |
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Rwork | 0.1787 | 21224 | - | - |
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all | 0.18 | - | - | - |
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obs | 0.1797 | 22332 | 80.328 % | - |
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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 BULK SOLVENT |
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原子変位パラメータ | Biso mean: 20.223 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.156 Å2 | -0 Å2 | -1.412 Å2 |
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2- | - | -1.523 Å2 | -0 Å2 |
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3- | - | - | 1.993 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.3→20.866 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1048 | 0 | 0 | 62 | 1110 |
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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_d0.008 | 0.013 | 1072 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.017 | 993 | X-RAY DIFFRACTION | r_angle_refined_deg1.378 | 1.634 | 1447 | X-RAY DIFFRACTION | r_angle_other_deg1.482 | 1.589 | 2308 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg4.632 | 5 | 134 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg42.934 | 26.122 | 49 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.704 | 15 | 195 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg12.835 | 15 | 1 | X-RAY DIFFRACTION | r_chiral_restr0.069 | 0.2 | 139 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 1208 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 218 | X-RAY DIFFRACTION | r_nbd_refined0.226 | 0.2 | 263 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.179 | 0.2 | 890 | X-RAY DIFFRACTION | r_nbtor_refined0.165 | 0.2 | 540 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.079 | 0.2 | 410 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.163 | 0.2 | 33 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.28 | 0.2 | 8 | X-RAY DIFFRACTION | r_nbd_other0.267 | 0.2 | 52 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.187 | 0.2 | 11 | X-RAY DIFFRACTION | r_mcbond_it1.792 | 1.72 | 539 | X-RAY DIFFRACTION | r_mcbond_other1.736 | 1.717 | 538 | X-RAY DIFFRACTION | r_mcangle_it2.341 | 2.591 | 672 | X-RAY DIFFRACTION | r_mcangle_other2.349 | 2.594 | 673 | X-RAY DIFFRACTION | r_scbond_it2.183 | 2.101 | 533 | X-RAY DIFFRACTION | r_scbond_other2.183 | 2.101 | 533 | X-RAY DIFFRACTION | r_scangle_it2.566 | 3.004 | 775 | X-RAY DIFFRACTION | r_scangle_other2.564 | 3.007 | 776 | X-RAY DIFFRACTION | r_lrange_it2.869 | 21.526 | 1241 | X-RAY DIFFRACTION | r_lrange_other2.863 | 21.424 | 1235 | X-RAY DIFFRACTION | r_rigid_bond_restr3.227 | 3 | 2065 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.3-1.334 | 0.249 | 43 | 0.223 | 736 | X-RAY DIFFRACTION | 38.2238 | 1.334-1.371 | 0.299 | 52 | 0.233 | 978 | X-RAY DIFFRACTION | 52.6585 | 1.371-1.41 | 0.323 | 56 | 0.182 | 1143 | X-RAY DIFFRACTION | 61.4242 | 1.41-1.454 | 0.193 | 60 | 0.166 | 1364 | X-RAY DIFFRACTION | 76.0684 | 1.454-1.501 | 0.212 | 84 | 0.155 | 1558 | X-RAY DIFFRACTION | 90.6181 | 1.501-1.554 | 0.158 | 98 | 0.15 | 1650 | X-RAY DIFFRACTION | 98.4234 | 1.554-1.613 | 0.185 | 97 | 0.139 | 1613 | X-RAY DIFFRACTION | 99.7666 | 1.613-1.678 | 0.148 | 72 | 0.138 | 1554 | X-RAY DIFFRACTION | 100 | 1.678-1.753 | 0.207 | 75 | 0.135 | 1498 | X-RAY DIFFRACTION | 100 | 1.753-1.838 | 0.146 | 81 | 0.144 | 1432 | X-RAY DIFFRACTION | 99.868 | 1.838-1.938 | 0.174 | 69 | 0.151 | 1353 | X-RAY DIFFRACTION | 99.7195 | 1.938-2.055 | 0.196 | 60 | 0.154 | 1269 | X-RAY DIFFRACTION | 96.7249 | 2.055-2.197 | 0.159 | 63 | 0.158 | 1118 | X-RAY DIFFRACTION | 92.2656 | 2.197-2.372 | 0.2 | 52 | 0.159 | 998 | X-RAY DIFFRACTION | 88.7574 | 2.372-2.598 | 0.179 | 45 | 0.176 | 878 | X-RAY DIFFRACTION | 83.5294 | 2.598-2.904 | 0.221 | 28 | 0.212 | 742 | X-RAY DIFFRACTION | 76.4648 | 2.904-3.351 | 0.226 | 30 | 0.226 | 538 | X-RAY DIFFRACTION | 64.9886 | 3.351-4.099 | 0.231 | 25 | 0.23 | 349 | X-RAY DIFFRACTION | 48.7614 | 4.099-5.778 | 0.293 | 11 | 0.26 | 295 | X-RAY DIFFRACTION | 52.0408 | 5.778-10 | 0.334 | 7 | 0.312 | 158 | X-RAY DIFFRACTION | 47.0085 |
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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 | 0.0656 | 0.2505 | -0.1299 | 2.1856 | -0.7705 | 0.3189 | -0.0249 | 0.0136 | 0.0088 | -0.0687 | 0.0419 | 0.0288 | 0.0431 | -0.0221 | -0.017 | 0.0202 | -0.0029 | 0.0063 | 0.0285 | 0.0002 | 0.0106 | 18.5704 | 19.4108 | 26.2747 | 2 | 0.3526 | 0.399 | -0.6808 | 0.667 | -0.762 | 1.3147 | -0.0143 | 0.0217 | 0.0078 | -0.002 | 0.0287 | 0.0299 | 0.0285 | -0.0402 | -0.0144 | 0.0145 | -0.001 | 0.0113 | 0.0266 | 0.0001 | 0.0129 | 14.3293 | 7.8622 | 39.0041 | 3 | 0.2304 | -0.141 | -0.1012 | 2.7024 | 0.3201 | 0.2958 | -0.0382 | -0.0424 | 0.0296 | 0.025 | 0.0179 | -0.0415 | 0.0175 | -0.029 | 0.0203 | 0.0212 | 0.003 | 0.0031 | 0.0362 | -0.007 | 0.0173 | 10.8259 | 6.3309 | 49.5272 | 4 | 0.0558 | 0.0165 | 0.1335 | 0.0049 | 0.0393 | 0.3203 | -0.0022 | -0.0023 | 0.0017 | -0.0001 | 0.0003 | 0.001 | -0.0079 | -0.0082 | 0.0019 | 0.0165 | 0.0012 | 0.0134 | 0.027 | 0.0001 | 0.0112 | 9.8619 | 20.2792 | 40.4301 | 5 | 0.4241 | -0.3666 | -0.2415 | 0.3273 | 0.1618 | 0.352 | -0.0054 | 0.0009 | 0.0061 | 0.0051 | 0.0019 | -0.0057 | 0.0087 | -0.0041 | 0.0035 | 0.0144 | -0.0012 | 0.0114 | 0.0253 | 0.0002 | 0.0093 | 18.5368 | 12.0128 | 45.9872 | 6 | 1.2957 | 0.3964 | -1.0434 | 2.0681 | -0.3786 | 3.6133 | 0.023 | -0.0411 | -0.0173 | 0.0501 | -0.031 | -0.0505 | -0.0493 | 0.0304 | 0.0079 | 0.0125 | -0.0003 | 0.0067 | 0.0274 | 0.0018 | 0.007 | 30.1223 | 11.4612 | 47.7809 | 7 | 0.003 | 0.0064 | -0.003 | 0.1465 | 0.0576 | 0.1849 | 0.0008 | 0.0033 | -0.0002 | -0.0046 | -0.0011 | -0.0038 | -0.0024 | 0.0025 | 0.0003 | 0.0152 | 0 | 0.0114 | 0.0251 | 0.0003 | 0.0089 | 29.8621 | 16.8186 | 33.7379 | 8 | 0.2911 | 0.5773 | -1.0778 | 1.3305 | -2.0242 | 4.5591 | 0.019 | -0.0175 | 0.0095 | 0.0402 | 0.0026 | -0.0172 | -0.0658 | 0.0315 | -0.0216 | 0.014 | -0.0006 | 0.0068 | 0.0292 | -0.0067 | 0.0147 | 28.1087 | 23.3209 | 53.3115 | 9 | 0.0402 | -0.0615 | 0.1043 | 0.2695 | -0.2812 | 0.3571 | -0.0024 | -0.0011 | -0.0013 | 0.017 | 0.0039 | -0.001 | -0.0185 | -0.0061 | -0.0015 | 0.0158 | 0.0004 | 0.0104 | 0.0256 | -0 | 0.0085 | 20.4926 | 22.6192 | 44.7351 | 10 | 0.3717 | 0.0348 | -0.3313 | 0.2451 | -0.0817 | 0.3167 | -0.0032 | 0.0127 | 0.0168 | 0.015 | 0.0086 | 0.0006 | 0.0136 | -0.0049 | -0.0053 | 0.0199 | 0.0015 | 0.0117 | 0.0256 | 0.0012 | 0.0084 | 18.6434 | 26.2781 | 30.5595 | 11 | 0.1159 | -0.0132 | -0.0163 | 0.0531 | -0.0349 | 0.0677 | -0.0011 | -0.0129 | 0.0067 | -0.0016 | -0.0013 | -0.0013 | 0.0026 | -0.0177 | 0.0024 | 0.0204 | -0.001 | 0.013 | 0.0348 | -0.0036 | 0.0089 | 20.4151 | 17.09 | 36.9089 |
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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 | ALLA24 - 35 | 2 | X-RAY DIFFRACTION | 2 | ALLA36 - 47 | 3 | X-RAY DIFFRACTION | 3 | ALLA48 - 55 | 4 | X-RAY DIFFRACTION | 4 | ALLA56 - 69 | 5 | X-RAY DIFFRACTION | 5 | ALLA70 - 88 | 6 | X-RAY DIFFRACTION | 6 | ALLA89 - 95 | 7 | X-RAY DIFFRACTION | 7 | ALLA96 - 125 | 8 | X-RAY DIFFRACTION | 8 | ALLA126 - 133 | 9 | X-RAY DIFFRACTION | 9 | ALLA134 - 151 | 10 | X-RAY DIFFRACTION | 10 | ALLA152 - 158 | 11 | X-RAY DIFFRACTION | 11 | ALLA201 - 262 | | | | | | | | | | | | | | | | | | | | | | |
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