ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | | 精密化 | SCALEPACK | | データスケーリング | PHASER | 2.6.0位相決定 | PDB_EXTRACT | 3.2 | データ抽出 | CrystalClear | | データ収集 | HKL-3000 | | データ削減 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4c1d 解像度: 1.93→23.99 Å / SU ML: 0.12 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 14.11
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1697 | 1438 | 9.98 % |
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Rwork | 0.1302 | - | - |
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obs | 0.1342 | 14407 | 98.35 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å |
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原子変位パラメータ | Biso max: 53.6 Å2 / Biso mean: 17.3166 Å2 / Biso min: 7.1 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.93→23.99 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1654 | 0 | 55 | 149 | 1858 |
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Biso mean | - | - | 31.22 | 28.31 | - |
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残基数 | - | - | - | - | 222 |
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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_d0.009 | 1751 | X-RAY DIFFRACTION | f_angle_d0.647 | 2381 | X-RAY DIFFRACTION | f_chiral_restr0.049 | 267 | X-RAY DIFFRACTION | f_plane_restr0.004 | 308 | X-RAY DIFFRACTION | f_dihedral_angle_d14.762 | 998 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.93-1.9989 | 0.1572 | 137 | 0.1192 | 1246 | 1383 | 97 | 1.9989-2.0789 | 0.1638 | 136 | 0.1128 | 1268 | 1404 | 98 | 2.0789-2.1735 | 0.1594 | 143 | 0.1161 | 1253 | 1396 | 97 | 2.1735-2.288 | 0.1509 | 141 | 0.1214 | 1266 | 1407 | 97 | 2.288-2.4312 | 0.1548 | 148 | 0.1235 | 1271 | 1419 | 98 | 2.4312-2.6187 | 0.1856 | 140 | 0.1256 | 1307 | 1447 | 99 | 2.6187-2.8818 | 0.1671 | 141 | 0.1291 | 1297 | 1438 | 99 | 2.8818-3.2979 | 0.1573 | 146 | 0.1253 | 1315 | 1461 | 99 | 3.2979-4.1515 | 0.1573 | 149 | 0.1244 | 1344 | 1493 | 99 | 4.1515-23.9917 | 0.2062 | 157 | 0.1612 | 1402 | 1559 | 99 |
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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 | 4.54 | 0.9406 | -0.5286 | 5.7636 | -0.8035 | 3.6119 | 0.0596 | -0.3068 | 0.0344 | 0.6868 | -0.0016 | 0.0382 | -0.2506 | -0.0753 | -0.0927 | 0.1041 | -0.0083 | 0.0106 | 0.1452 | -0.0059 | 0.0353 | -7.0201 | 18.5302 | -2.3421 | 2 | 2.4471 | -0.5436 | -0.3641 | 3.7788 | 0.1605 | 1.8514 | 0.0726 | 0.0282 | 0.1096 | -0.0458 | -0.0374 | -0.0293 | -0.1225 | 0.0152 | -0.0108 | 0.0666 | -0.0147 | 0.0026 | 0.0538 | -0.0089 | 0.0405 | -2.9042 | 18.2775 | -9.0457 | 3 | 0.71 | -0.328 | 0.4203 | 1.4563 | -1.2992 | 3.0403 | 0.0056 | -0.0586 | 0.0022 | 0.0602 | -0.0012 | -0.0273 | 0.0038 | 0.0356 | -0.0097 | 0.0553 | -0.0145 | 0.0057 | 0.0848 | -0.0115 | 0.0909 | 2.487 | 17.9217 | -8.6523 | 4 | 3.2785 | 0.4345 | 0.0692 | 4.5437 | -0.298 | 2.9533 | 0.0694 | 0.1112 | 0.0107 | -0.0534 | -0.1575 | -0.203 | -0.06 | 0.1151 | 0.0702 | 0.0429 | -0.0043 | 0.0235 | 0.0958 | 0.0029 | 0.1005 | 7.919 | 18.2362 | -19.9939 | 5 | 2.0364 | 0.5735 | -0.2319 | 1.3684 | -0.4296 | 0.83 | -0.0145 | 0.18 | -0.2509 | -0.0319 | 0.018 | -0.0145 | 0.1259 | -0.0342 | -0.011 | 0.1004 | -0.0055 | 0.0067 | 0.0903 | -0.0267 | 0.0855 | -2.7176 | 9.7714 | -20.669 | 6 | 3.9777 | -0.2491 | -1.3183 | 0.7667 | -0.2742 | 3.7288 | -0.0657 | 0.2841 | 0.4666 | -0.0511 | -0.094 | 0.0208 | -0.2964 | -0.1146 | -0.0001 | 0.1255 | -0.0114 | -0.0233 | 0.1436 | 0.0163 | 0.1579 | -15.378 | 23.0058 | -21.743 | 7 | 2.0303 | 0.9561 | -0.6767 | 3.2909 | -4.6705 | 7.8246 | -0.0145 | 0.5072 | -0.1901 | -0.5153 | 0.0885 | 0.37 | 0.5165 | -0.4147 | -0.1269 | 0.1404 | -0.0002 | -0.0263 | 0.2419 | -0.0511 | 0.1391 | -14.917 | 10.3561 | -27.5574 | 8 | 3.5556 | 0.4565 | 0.39 | 4.8514 | 1.959 | 4.9286 | -0.0271 | -0.0139 | -0.2498 | 0.3862 | -0.0033 | 0.282 | 0.3194 | -0.173 | 0.039 | 0.0591 | -0.005 | 0.0118 | 0.1056 | 0.0012 | 0.0857 | -14.4946 | 11.1105 | -12.7048 | 9 | 4.5035 | -0.993 | 0.6427 | 7.3846 | -4.8522 | 3.4048 | 0.0309 | 0.3029 | -0.0122 | -0.2833 | 0.0525 | 0.1511 | 0.1002 | -0.2581 | -0.1402 | 0.0993 | -0.0036 | -0.0024 | 0.1394 | -0.01 | 0.1081 | -21.261 | 16.6408 | -22.6871 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 39 through 52 )A39 - 52 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 53 through 88 )A53 - 88 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 89 through 122 )A89 - 122 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 123 through 146 )A123 - 146 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 147 through 199 )A147 - 199 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 200 through 215 )A200 - 215 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 216 through 229 )A216 - 229 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 230 through 245 )A230 - 245 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 246 through 260 )A246 - 260 | | | | | | | | | | | | | | | | | | |
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