ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALEPACK | | データスケーリング | | PHENIX | 1.7.3_928精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.4→41.01 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.2 / σ(F): 1.34 / 位相誤差: 18.5 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.198 | 7379 | 10 % |
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Rwork | 0.175 | - | - |
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obs | 0.178 | 73824 | 96.3 % |
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溶媒の処理 | 減衰半径: 0.73 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 49.01 Å2 / ksol: 0.39 e/Å3 |
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原子変位パラメータ | Biso mean: 31.13 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.4→41.01 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2577 | 0 | 0 | 339 | 2916 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.005 | 2726 | X-RAY DIFFRACTION | f_angle_d1.001 | 3710 | X-RAY DIFFRACTION | f_dihedral_angle_d14.639 | 996 | X-RAY DIFFRACTION | f_chiral_restr0.131 | 390 | X-RAY DIFFRACTION | f_plane_restr0.004 | 488 | | | | | |
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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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1.4-1.4143 | 0.3757 | 218 | 0.3712 | 1986 | X-RAY DIFFRACTION | 87 | 1.4143-1.431 | 0.3865 | 234 | 0.3599 | 2145 | X-RAY DIFFRACTION | 94 | 1.431-1.4484 | 0.3097 | 242 | 0.3285 | 2160 | X-RAY DIFFRACTION | 94 | 1.4484-1.4668 | 0.3412 | 239 | 0.2976 | 2136 | X-RAY DIFFRACTION | 95 | 1.4668-1.4861 | 0.2794 | 241 | 0.2743 | 2143 | X-RAY DIFFRACTION | 95 | 1.4861-1.5064 | 0.2315 | 242 | 0.2555 | 2147 | X-RAY DIFFRACTION | 95 | 1.5064-1.5279 | 0.2357 | 241 | 0.2427 | 2193 | X-RAY DIFFRACTION | 95 | 1.5279-1.5507 | 0.2737 | 229 | 0.2193 | 2171 | X-RAY DIFFRACTION | 95 | 1.5507-1.575 | 0.1871 | 249 | 0.2185 | 2167 | X-RAY DIFFRACTION | 96 | 1.575-1.6008 | 0.243 | 247 | 0.2081 | 2185 | X-RAY DIFFRACTION | 96 | 1.6008-1.6284 | 0.2333 | 237 | 0.1895 | 2191 | X-RAY DIFFRACTION | 96 | 1.6284-1.658 | 0.1925 | 247 | 0.1796 | 2191 | X-RAY DIFFRACTION | 96 | 1.658-1.6899 | 0.1903 | 243 | 0.176 | 2192 | X-RAY DIFFRACTION | 96 | 1.6899-1.7244 | 0.1963 | 245 | 0.1769 | 2199 | X-RAY DIFFRACTION | 96 | 1.7244-1.7619 | 0.2115 | 247 | 0.1733 | 2229 | X-RAY DIFFRACTION | 97 | 1.7619-1.8029 | 0.204 | 246 | 0.175 | 2180 | X-RAY DIFFRACTION | 97 | 1.8029-1.848 | 0.1937 | 253 | 0.1734 | 2257 | X-RAY DIFFRACTION | 97 | 1.848-1.8979 | 0.1808 | 245 | 0.1671 | 2200 | X-RAY DIFFRACTION | 97 | 1.8979-1.9538 | 0.1788 | 252 | 0.1665 | 2252 | X-RAY DIFFRACTION | 97 | 1.9538-2.0168 | 0.181 | 250 | 0.1669 | 2233 | X-RAY DIFFRACTION | 98 | 2.0168-2.0889 | 0.1728 | 246 | 0.1606 | 2246 | X-RAY DIFFRACTION | 98 | 2.0889-2.1726 | 0.1915 | 247 | 0.1614 | 2240 | X-RAY DIFFRACTION | 98 | 2.1726-2.2714 | 0.1711 | 252 | 0.1529 | 2283 | X-RAY DIFFRACTION | 98 | 2.2714-2.3912 | 0.1652 | 251 | 0.1484 | 2266 | X-RAY DIFFRACTION | 98 | 2.3912-2.541 | 0.178 | 253 | 0.1569 | 2286 | X-RAY DIFFRACTION | 99 | 2.541-2.7371 | 0.2032 | 251 | 0.1626 | 2299 | X-RAY DIFFRACTION | 99 | 2.7371-3.0125 | 0.1983 | 257 | 0.1787 | 2297 | X-RAY DIFFRACTION | 99 | 3.0125-3.4482 | 0.1861 | 258 | 0.1675 | 2325 | X-RAY DIFFRACTION | 98 | 3.4482-4.3436 | 0.1675 | 256 | 0.1536 | 2305 | X-RAY DIFFRACTION | 97 | 4.3436-41.0262 | 0.2359 | 261 | 0.1936 | 2341 | X-RAY DIFFRACTION | 94 |
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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 | 4.4128 | 1.9581 | 0.9061 | 3.081 | -0.3795 | 0.4618 | 0.2184 | -0.5604 | -0.0902 | 0.1383 | -0.5167 | -0.1619 | 0.2342 | 0.0177 | 0.2549 | 0.2886 | 0.0556 | 0.101 | 0.3117 | 0.1031 | 0.2765 | 25.9309 | 1.7735 | 4.0535 | 2 | 3.7146 | -1.3525 | -0.0295 | 4.4711 | -1.3585 | 3.1416 | 0.0013 | 0.3438 | -0.2003 | -0.5335 | -0.102 | 0.1346 | 0.3856 | -0.0964 | 0.0737 | 0.2185 | 0.0184 | 0.0426 | 0.1536 | -0.0186 | 0.1479 | 12.2132 | 2.5848 | -5.9708 | 3 | 2.7021 | -0.2663 | -1.0588 | 2.5899 | -1.6972 | 4.3647 | -0.0431 | -0.0949 | 0.2306 | 0.1334 | -0.2345 | -0.5499 | -0.0743 | 0.5466 | 0.2764 | 0.2173 | 0.0109 | 0.0149 | 0.2808 | 0.115 | 0.3088 | 23.0298 | 2.6837 | 6.5191 | 4 | 5.037 | 0.247 | 0.237 | 3.3679 | -0.8736 | 3.0817 | -0.1445 | -0.5045 | -0.484 | 0.2254 | 0.2644 | 0.4381 | 0.1365 | -0.5014 | 0.0028 | 0.2231 | 0.0075 | 0.0635 | 0.2876 | 0.1166 | 0.3015 | 6.8061 | -0.5901 | 9.308 | 5 | 2.5933 | -0.9485 | -0.0816 | 2.6952 | -0.9515 | 2.23 | -0.0743 | -0.1662 | -0.0455 | 0.0979 | 0.0876 | 0.0583 | 0.033 | -0.1706 | -0.0066 | 0.116 | -0.0097 | 0.02 | 0.1502 | 0.0034 | 0.1287 | 6.7565 | 9.5187 | 3.7977 | 6 | 8.2822 | 0.0975 | -2.7939 | 3.8155 | -1.5457 | 6.9315 | -0.046 | -1.0666 | 0.4036 | 0.537 | -0.0782 | -0.5368 | -0.5912 | 0.8499 | 0.2001 | 0.3376 | -0.0278 | -0.0685 | 0.5335 | -0.0414 | 0.276 | 15.6674 | 17.8831 | 13.3151 | 7 | 3.9724 | -0.446 | -0.4513 | 2.9859 | -1.4744 | 5.0808 | -0.0329 | 0.145 | 0.5903 | 0.0215 | -0.1301 | -0.0766 | -0.6488 | 0.1247 | 0.0348 | 0.1996 | 0.0116 | 0.0164 | 0.148 | 0.0182 | 0.2739 | 10.6656 | 24.2626 | -0.7956 | 8 | 3.4146 | -0.7265 | -0.33 | 5.5407 | 1.058 | 3.9823 | -0.1848 | -0.1702 | 0.0467 | 0.2146 | 0.1264 | 0.5077 | -0.1675 | -0.3894 | 0.0581 | 0.2082 | 0.0094 | 0.0273 | 0.279 | -0.0021 | 0.1752 | -22.8189 | 13.9784 | 23.017 | 9 | 2.0664 | -0.6595 | -0.0405 | 3.0219 | 0.6213 | 1.8629 | -0.1926 | -0.4661 | 0.1557 | 0.1656 | 0.184 | -0.0676 | -0.2509 | -0.025 | 0.0406 | 0.2693 | 0.0625 | 0.0285 | 0.2156 | -0.0266 | 0.156 | -15.2969 | 14.5101 | 27.4188 | 10 | 5.1024 | -0.6765 | -0.7693 | 4.9525 | 0.1093 | 6.1894 | -0.1985 | -0.0216 | 0.478 | 0.233 | 0.0296 | -0.3881 | -0.5606 | 0.3709 | -0.028 | 0.2162 | -0.0084 | -0.0402 | 0.1901 | 0.0094 | 0.2283 | -9.447 | 19.9602 | 17.3957 | 11 | 3.9938 | 1.2069 | -0.2056 | 7.1166 | 1.1315 | 3.9331 | -0.0853 | 0.5564 | 0.0074 | -0.4398 | 0.2359 | -0.3925 | 0.0077 | 0.5445 | -0.0217 | 0.1889 | 0.0137 | 0.0162 | 0.2189 | 0.0203 | 0.1851 | -8.1762 | 12.3587 | 8.455 | 12 | 2.0266 | 0.1287 | 0.0344 | 4.194 | 0.5633 | 2.7654 | -0.1513 | 0.0826 | 0.0546 | 0.0665 | 0.144 | 0.2274 | 0.153 | -0.2034 | -0.03 | 0.1537 | -0.0141 | -0.008 | 0.163 | 0.0148 | 0.147 | -15.3798 | 13.9728 | 9.611 | 13 | 6.2141 | -2.5736 | 1.8405 | 3.5774 | -1.3984 | 2.9614 | 0.0789 | 0.2708 | -0.3471 | -0.1163 | -0.0175 | 0.0705 | 0.4643 | 0.0966 | -0.039 | 0.1821 | 0.0147 | 0.0213 | 0.1229 | -0.0061 | 0.1163 | -10.5061 | 4.1188 | 17.951 | 14 | 2.0935 | 0.0177 | 0.4767 | 2.8389 | -0.2315 | 1.7931 | -0.1404 | 0.0452 | -0.07 | 0.2445 | 0.1651 | -0.2966 | 0.3835 | 0.4183 | -0.0291 | 0.2445 | 0.0981 | -0.0082 | 0.2243 | -0.0193 | 0.1907 | -0.1396 | 4.2528 | 24.7192 | 15 | 3.7137 | 2.0421 | -2.2043 | 5.0265 | -1.1178 | 2.2835 | 0.2759 | -0.0343 | 0.7448 | 0.2926 | -0.0656 | -0.6306 | -0.3526 | 0.6605 | -0.2662 | 0.2978 | 0.0197 | -0.0469 | 0.3216 | -0.0449 | 0.3951 | 4.6059 | 16.0297 | 26.0974 | 16 | 4.4382 | -2.0818 | 0.5099 | 4.305 | -1.024 | 1.1258 | -0.0772 | -0.4155 | -0.1587 | 0.5808 | 0.2219 | -0.2102 | 0.1637 | -0.0787 | -0.191 | 0.3352 | 0.1477 | -0.0916 | 0.2697 | -0.0638 | 0.1734 | 1.8284 | 3.512 | 33.4119 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resseq 48:72)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 73:92)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 93:112)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 113:132)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 133:192)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 193:202)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 203:220)8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq 61:81)9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 82:106)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 107:118)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 119:127)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 128:141)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 142:163)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 164:191)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 192:200)16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resseq 201:220) | | | | | | | | | | | | | | | |
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