ソフトウェア | 名称 | バージョン | 分類 |
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AMoRE | | 位相決定 | REFMAC | 5.2.0019精密化 | XDS | | データ削減 | XDS | | データスケーリング | |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: PDB ENTRY 2IGO 解像度: 1.55→53.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.399 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / 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 | 0.21883 | 2899 | 3 % | RANDOM |
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Rwork | 0.18602 | - | - | - |
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obs | 0.18703 | 93323 | 99.77 % | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 9.57 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.18 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.18 Å2 | 0 Å2 |
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3- | - | - | 0.35 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.55→53.8 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4538 | 0 | 65 | 470 | 5073 |
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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_d0.022 | 0.022 | 4724 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 3188 | X-RAY DIFFRACTION | r_angle_refined_deg1.981 | 1.963 | 6423 | X-RAY DIFFRACTION | r_angle_other_deg1.054 | 3 | 7765 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.945 | 5 | 575 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.119 | 24.464 | 224 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.86 | 15 | 760 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.412 | 15 | 27 | X-RAY DIFFRACTION | r_chiral_restr0.208 | 0.2 | 696 | X-RAY DIFFRACTION | r_gen_planes_refined0.009 | 0.02 | 5239 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 946 | X-RAY DIFFRACTION | r_nbd_refined0.222 | 0.2 | 974 | X-RAY DIFFRACTION | r_nbd_other0.215 | 0.2 | 3475 | X-RAY DIFFRACTION | r_nbtor_refined0.192 | 0.2 | 2351 | X-RAY DIFFRACTION | r_nbtor_other0.097 | 0.2 | 2561 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.168 | 0.2 | 333 | 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_refined0.2 | 0.2 | 13 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.223 | 0.2 | 71 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.146 | 0.2 | 21 | 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_it1.4 | 1.5 | 3589 | X-RAY DIFFRACTION | r_mcbond_other0.366 | 1.5 | 1153 | X-RAY DIFFRACTION | r_mcangle_it1.698 | 2 | 4673 | X-RAY DIFFRACTION | r_scbond_it2.955 | 3 | 2115 | X-RAY DIFFRACTION | r_scangle_it4.069 | 4.5 | 1750 | 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: 1.55→1.634 Å / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.311 | 399 | - |
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Rwork | 0.265 | 13283 | - |
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obs | - | - | 98.45 % |
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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 | 13.7579 | 1.3763 | -6.1903 | 0.6444 | -1.9049 | 6.0471 | -0.0599 | 0.673 | -0.9136 | 0.0142 | -0.1039 | -0.1335 | 0.343 | -0.4536 | 0.1638 | 0.0584 | -0.0225 | 0.0062 | 0.0475 | -0.0844 | 0.0254 | 70.2711 | 40.3169 | 13.352 | 2 | 0.3731 | -0.1136 | 0.012 | 0.3031 | -0.131 | 0.0608 | 0.0134 | 0.0528 | 0.0033 | -0.0058 | 0.0101 | 0.0565 | 0.0007 | -0.0058 | -0.0235 | 0.0209 | 0.0004 | 0.0075 | 0.0381 | -0.004 | -0.011 | 66.7523 | 50.73 | 22.3974 | 3 | 0.102 | -0.0032 | 0.0022 | 0.0582 | -0.0207 | 0.0074 | -0.0153 | -0.0071 | 0.0016 | 0.0226 | 0.0023 | -0.0137 | -0.0181 | 0.0035 | 0.0129 | 0.0314 | -0.0025 | 0.0063 | 0.019 | 0.0018 | 0.0029 | 54.9788 | 44.4225 | 48.8733 | 4 | 0.0643 | -0.0474 | 0.1282 | 0.2216 | -0.2391 | 0.3678 | -0.0122 | 0.0047 | 0.0021 | -0.0015 | -0.0092 | -0.0117 | 0.009 | -0.0079 | 0.0214 | 0.0189 | 0.0046 | 0.0095 | 0.0233 | -0.0001 | 0.0036 | 66.8701 | 46.4055 | 44.1709 | 5 | 1.7404 | -0.0439 | 0.1791 | 0.3302 | -0.2737 | 0.9688 | 0.0247 | 0.0177 | 0.0371 | -0.0214 | -0.0416 | -0.0302 | -0.0202 | 0.0857 | 0.0168 | 0.0223 | -0.0176 | 0.02 | 0.0065 | 0.0064 | 0.0057 | 82.8375 | 66.5331 | 33.0526 | 6 | 0.6107 | -0.2685 | -0.4544 | 0.5413 | 0.7819 | 1.1386 | 0.0398 | 0.0375 | 0.0418 | -0.0108 | -0.0553 | -0.0279 | 0.0089 | -0.0959 | 0.0155 | 0.0279 | 0.0029 | 0.0074 | 0.0074 | 0.0157 | 0.0013 | 61.6526 | 75.5422 | 39.15 | 7 | 5.2509 | -3.2444 | 0.5271 | 3.5262 | 1.7041 | 2.7606 | -0.0794 | -0.0817 | 0.2631 | -0.0955 | 0.1767 | -0.1793 | -0.1903 | 0.0337 | -0.0973 | 0.021 | -0.0338 | -0.0103 | -0.0113 | 0.0085 | 0.0155 | 71.9783 | 81.1164 | 52.1015 | 8 | 0.0748 | -0.1888 | -0.1593 | 0.4914 | 0.3821 | 0.365 | 0.0034 | 0.0491 | 0.009 | -0.0274 | -0.0351 | 0.0424 | -0.0394 | 0.0086 | 0.0317 | 0.0223 | 0.0031 | 0.009 | 0.0153 | 0.0088 | 0.0107 | 60.1385 | 66.4001 | 31.0671 | 9 | 0.5322 | 0.1043 | -0.3502 | 0.0407 | -0.0489 | 0.2495 | 0.0267 | 0.1419 | -0.0341 | -0.0163 | 0.0155 | 0.0624 | 0.0264 | -0.0377 | -0.0423 | 0.0249 | 0.0011 | -0.0003 | 0.0381 | -0.0111 | -0.0127 | 64.5561 | 47.7143 | 16.4615 | 10 | 1.7573 | -0.4854 | -0.6103 | 0.1951 | 0.3712 | 0.8854 | 0.0447 | 0.1012 | -0.0463 | -0.0102 | -0.0739 | -0.0051 | 0.0277 | -0.0125 | 0.0292 | 0.0253 | 0.0101 | 0.034 | 0.0157 | -0.0248 | 0.0167 | 82.411 | 35.7906 | 23.3414 | 11 | 12.7008 | -3.2994 | -3.7317 | 4.2483 | 0.4686 | 1.1704 | 0.097 | 0.5413 | -0.4635 | -0.0678 | -0.0192 | 0.0041 | 0.1462 | -0.3035 | -0.0778 | 0.0262 | -0.0218 | -0.0231 | -0.0186 | -0.054 | 0.0262 | 63.7961 | 32.4239 | 23.9803 | 12 | 0.037 | 0.0739 | -0.0537 | 0.1792 | 0.0097 | 0.5121 | -0.0097 | 0.0033 | -0.0327 | -0.0153 | -0.0234 | -0.0059 | 0.0421 | 0.08 | 0.0332 | 0.017 | 0.0145 | 0.0154 | 0.0199 | -0.0014 | 0.0163 | 80.5565 | 40.1274 | 35.51 | 13 | 0.7682 | -0.5425 | 0.1257 | 0.7941 | 0.0228 | 0.0509 | -0.0686 | -0.0056 | 0.1144 | 0.022 | -0.0002 | -0.0591 | 0.0362 | -0.0214 | 0.0687 | 0.0119 | 0.0138 | -0.0111 | 0.0211 | 0.0067 | 0.0129 | 56.4731 | 77.3969 | 53.6219 | 14 | 7.1185 | -1.9956 | -1.1408 | 1.7087 | -1.139 | 2.0347 | -0.0928 | 0.2182 | 0.9988 | 0.2349 | 0.0909 | -0.3854 | -0.0497 | -0.2098 | 0.0019 | -0.0462 | 0.0157 | -0.0571 | -0.0659 | 0.025 | 0.115 | 46.0942 | 92.7171 | 47.5377 | 15 | 1.1825 | -0.5899 | -0.0567 | 0.308 | -0.0235 | 0.1984 | -0.0484 | 0.0701 | 0.0059 | -0.0021 | 0.009 | -0.0025 | 0.002 | -0.0249 | 0.0394 | 0.0099 | -0.0001 | -0.0087 | 0.016 | 0.0072 | 0.0066 | 56.1235 | 76.6588 | 46.642 | 16 | 0.45 | 1.5635 | 0.0848 | 5.4322 | 0.2947 | 0.016 | -0.6846 | -0.7618 | -0.1171 | -0.6437 | 0.8186 | 0.2601 | 1.1174 | 1.0195 | -0.134 | 0.1259 | 0.0028 | -0.0052 | 0.1289 | -0.0003 | 0.1299 | 51.4973 | 61.3299 | 52.5396 | 17 | 0.4119 | -0.1118 | -0.1921 | 0.0325 | 0.0523 | 0.0896 | -0.0113 | 0.034 | 0.0269 | -0.0107 | 0.0189 | 0.0002 | 0.0295 | -0.0043 | -0.0076 | 0.0188 | 0.0069 | 0.0045 | 0.0314 | -0.0002 | 0.0045 | 59.8939 | 66.9117 | 51.859 | 18 | 0.9014 | 0.5852 | 0.7097 | 1.1021 | 0.4452 | 0.5591 | 0.0212 | -0.0067 | -0.0806 | 0.0236 | 0.0241 | -0.0305 | 0.0037 | 0.0032 | -0.0452 | 0.0101 | -0.0003 | 0.0246 | 0.0183 | 0.0064 | 0.0082 | 75.5255 | 39.7708 | 45.3236 | 19 | 0.4 | -0.2213 | -0.1166 | 0.1466 | 0.1344 | 0.2357 | -0.0259 | -0.0129 | -0.001 | 0.0217 | 0.0164 | -0.002 | 0.01 | 0.0069 | 0.0095 | 0.0196 | 0.004 | 0.0045 | 0.0222 | 0.004 | 0.0042 | 69.6402 | 63.1379 | 57.36 | 20 | 0.1765 | -0.0483 | -0.1513 | 0.1838 | 0.0463 | 0.2833 | -0.0096 | 0.0043 | -0.0125 | -0.0057 | 0.0008 | -0.0344 | -0.0161 | 0.0049 | 0.0088 | 0.0143 | -0.0018 | 0.0154 | 0.0201 | -0.001 | 0.0095 | 81.8031 | 52.7123 | 29.7754 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A43 - 48 | 2 | X-RAY DIFFRACTION | 2 | A49 - 86 | 3 | X-RAY DIFFRACTION | 3 | A87 - 140 | 4 | X-RAY DIFFRACTION | 4 | A141 - 171 | 5 | X-RAY DIFFRACTION | 5 | A172 - 204 | 6 | X-RAY DIFFRACTION | 6 | A205 - 225 | 7 | X-RAY DIFFRACTION | 7 | A226 - 235 | 8 | X-RAY DIFFRACTION | 8 | A236 - 263 | 9 | X-RAY DIFFRACTION | 9 | A264 - 285 | 10 | X-RAY DIFFRACTION | 10 | A286 - 299 | 11 | X-RAY DIFFRACTION | 11 | A300 - 310 | 12 | X-RAY DIFFRACTION | 12 | A311 - 357 | 13 | X-RAY DIFFRACTION | 13 | A358 - 383 | 14 | X-RAY DIFFRACTION | 14 | A384 - 407 | 15 | X-RAY DIFFRACTION | 15 | A408 - 451 | 16 | X-RAY DIFFRACTION | 16 | A452 - 460 | 17 | X-RAY DIFFRACTION | 17 | A461 - 477 | 18 | X-RAY DIFFRACTION | 18 | A478 - 505 | 19 | X-RAY DIFFRACTION | 19 | A506 - 545 | 20 | X-RAY DIFFRACTION | 20 | A546 - 618 | | | | | | | | | | | | | | | | | | | | |
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