ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.9_1692精密化 | HKL-2000 | | データ収集 | HKL-2000 | | データスケーリング | AutoSol | | 位相決定 | PDB_EXTRACT | 3.25 | データ抽出 | PHENIX | | モデル構築 | BUCCANEER | | モデル構築 | HKL-2000 | | データ削減 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.501→31.641 Å / SU ML: 0.44 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 31.45 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2727 | 3958 | 2.19 % |
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Rwork | 0.2417 | 177057 | - |
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obs | 0.2424 | 181015 | 99.21 % |
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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 / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 329.3 Å2 / Biso mean: 82.1693 Å2 / Biso min: 32.32 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.501→31.641 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 13296 | 0 | 0 | 36 | 13332 |
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Biso mean | - | - | - | 55.14 | - |
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残基数 | - | - | - | - | 1726 |
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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_d0.003 | 13534 | X-RAY DIFFRACTION | f_angle_d0.81 | 18340 | X-RAY DIFFRACTION | f_chiral_restr0.032 | 2093 | X-RAY DIFFRACTION | f_plane_restr0.004 | 2364 | X-RAY DIFFRACTION | f_dihedral_angle_d13.163 | 4762 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | Rms | タイプ |
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1 | 1 | A7397 | X-RAY DIFFRACTION | 9.89 | TORSIONAL1 | 2 | B7397 | X-RAY DIFFRACTION | 9.89 | TORSIONAL1 | 3 | C7397 | X-RAY DIFFRACTION | 9.89 | TORSIONAL1 | 4 | D7397 | X-RAY DIFFRACTION | 9.89 | TORSIONAL | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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2.5012-2.5317 | 0.349 | 137 | 0.341 | 6049 | 94 | 2.5317-2.5638 | 0.3954 | 137 | 0.3369 | 6211 | 98 | 2.5638-2.5975 | 0.3835 | 142 | 0.3313 | 6270 | 98 | 2.5975-2.633 | 0.374 | 140 | 0.3347 | 6270 | 99 | 2.633-2.6706 | 0.3955 | 140 | 0.3337 | 6262 | 99 | 2.6706-2.7105 | 0.3559 | 139 | 0.3344 | 6305 | 99 | 2.7105-2.7528 | 0.3804 | 143 | 0.3227 | 6384 | 99 | 2.7528-2.7979 | 0.3719 | 138 | 0.3212 | 6263 | 99 | 2.7979-2.8461 | 0.3643 | 139 | 0.3158 | 6283 | 99 | 2.8461-2.8979 | 0.3179 | 140 | 0.2986 | 6285 | 99 | 2.8979-2.9536 | 0.3247 | 146 | 0.297 | 6378 | 99 | 2.9536-3.0138 | 0.3417 | 142 | 0.2971 | 6369 | 99 | 3.0138-3.0793 | 0.3665 | 138 | 0.293 | 6261 | 99 | 3.0793-3.1508 | 0.3202 | 146 | 0.2798 | 6382 | 99 | 3.1508-3.2296 | 0.3041 | 140 | 0.2806 | 6352 | 100 | 3.2296-3.3168 | 0.3286 | 140 | 0.2723 | 6343 | 100 | 3.3168-3.4143 | 0.3033 | 140 | 0.2489 | 6322 | 100 | 3.4143-3.5244 | 0.2802 | 143 | 0.2462 | 6385 | 100 | 3.5244-3.6501 | 0.2935 | 145 | 0.2323 | 6346 | 100 | 3.6501-3.7961 | 0.2416 | 140 | 0.2326 | 6337 | 100 | 3.7961-3.9685 | 0.2136 | 144 | 0.2233 | 6426 | 100 | 3.9685-4.1773 | 0.2738 | 141 | 0.2116 | 6344 | 100 | 4.1773-4.4384 | 0.2489 | 143 | 0.2068 | 6402 | 100 | 4.4384-4.78 | 0.1911 | 142 | 0.1918 | 6359 | 100 | 4.78-5.259 | 0.2336 | 144 | 0.2023 | 6358 | 100 | 5.259-6.0155 | 0.2754 | 143 | 0.2334 | 6398 | 100 | 6.0155-7.5618 | 0.3128 | 143 | 0.2463 | 6359 | 100 | 7.5618-31.641 | 0.1923 | 143 | 0.2067 | 6354 | 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 | 1.4312 | 1.1242 | 1.5481 | 3.9572 | 1.2267 | 1.9229 | -0.1674 | 0.4112 | 0.1353 | -0.3272 | 0.0251 | -0.0068 | -0.0533 | -0.1082 | 0.1881 | 0.4651 | 0.0138 | 0.1308 | 0.5711 | 0.0444 | 0.3902 | -24.7185 | 23.4043 | -9.747 | 2 | 2.9506 | 0.0357 | -1.1978 | 1.4198 | 0.4102 | 3.2418 | -0.3469 | 0.5389 | -0.2785 | -0.0189 | 0.0154 | 0.14 | 0.6905 | -0.5114 | 0.2985 | 0.6453 | -0.1405 | 0.1082 | 0.4967 | -0.061 | 0.417 | -33.7342 | 9.176 | -6.5766 | 3 | 3.9019 | 0.2635 | 1.5147 | 5.8191 | 1.5842 | 6.7264 | -0.3119 | 0.9457 | -0.1022 | -0.7686 | -0.1021 | 0.3521 | 0.3807 | -0.598 | 0.4148 | 0.6385 | -0.1563 | 0.1797 | 0.8792 | -0.0781 | 0.5212 | -58.5357 | 12.0181 | 5.6255 | 4 | 4.2031 | 1.9759 | 2.026 | 6.7374 | 1.0067 | 3.6115 | 0.092 | -0.5647 | -0.7521 | 0.3516 | -0.0894 | -0.2408 | 0.8041 | -0.1563 | -0.033 | 0.6041 | -0.0413 | 0.2095 | 0.5916 | 0.1494 | 0.5255 | -17.3965 | 3.1948 | 17.638 | 5 | 5.5509 | 0.0081 | 1.1832 | 0.7117 | 0.005 | 0.0825 | -0.0588 | -0.4684 | -0.0737 | 0.0485 | 0.0553 | -0.082 | -0.0447 | 0.1068 | 0.0503 | 0.5531 | 0.0107 | 0.1511 | 0.6308 | 0.0817 | 0.409 | -6.579 | 12.304 | 20.4203 | 6 | 3.0281 | -2.4509 | -0.1295 | 1.969 | 0.1172 | 0.0774 | 0.0327 | -1.0755 | 1.4176 | 1.0313 | 0.1191 | 0.4662 | -0.5616 | -0.3836 | 0.0701 | 0.7251 | 0.0089 | 0.1658 | 0.9481 | -0.3721 | 0.9093 | -49.2497 | 31.2022 | 31.9122 | 7 | 4.2868 | 0.3428 | 0.4196 | 3.0764 | 0.0653 | 4.3382 | 0.0397 | -1.1105 | 0.2837 | 0.3701 | -0.1336 | -0.0706 | 0.3886 | 0.2763 | 0.1425 | 0.6477 | -0.04 | 0.225 | 1.069 | -0.1422 | 0.4953 | -42.4409 | 20.2286 | 33.1403 | 8 | 2.1831 | -0.5155 | 0.5599 | 2.8813 | -0.6454 | 2.2099 | -0.0954 | -0.5049 | 0.1602 | 0.3473 | 0.1045 | 0.1564 | -0.0832 | -0.2135 | -0.0403 | 0.4667 | 0.0362 | 0.1622 | 0.4883 | -0.0232 | 0.4383 | -22.3278 | 46.6075 | 9.1666 | 9 | 2.4047 | -0.0584 | 0.8186 | 1.0295 | 0.5972 | 2.6881 | -0.3305 | -1.0581 | 0.1802 | 0.14 | 0.0896 | 0.2108 | -0.5193 | -0.9575 | 0.145 | 0.6931 | 0.2295 | 0.2067 | 0.7381 | -0.1514 | 0.7607 | -40.3645 | 60.0218 | 9.1455 | 10 | 6.2341 | 0.0978 | -0.5445 | 3.4359 | 0.4128 | 6.5183 | -0.1012 | -0.4951 | -0.7396 | 0.3452 | -0.2548 | 0.6221 | -0.1856 | -0.9847 | 0.3819 | 0.6226 | 0.1656 | 0.1016 | 0.7452 | -0.1341 | 0.8401 | -57.5835 | 56.4872 | -9.0575 | 11 | 5.5722 | -0.8343 | -0.8688 | 2.2906 | 0.3334 | 3.5623 | 0.0245 | 0.8038 | 1.1049 | -0.5087 | -0.0579 | 0.0912 | -0.8349 | 0.0687 | 0.0797 | 0.5619 | 0.0131 | 0.0153 | 0.416 | 0.2328 | 0.6074 | -15.5215 | 63.2245 | -17.0253 | 12 | 6.1134 | -0.4429 | -0.5499 | 1.0888 | 0.6614 | 1.7341 | -0.0474 | 1.0973 | 0.3007 | -0.3669 | -0.1278 | -0.1235 | -0.347 | 0.4733 | 0.0575 | 0.6592 | 0.0359 | 0.0871 | 0.66 | 0.1535 | 0.5238 | -5.8696 | 54.0664 | -23.4411 | 13 | 5.175 | -0.1779 | -2.5782 | 4.1544 | 1.0924 | 5.9963 | -0.0448 | 1.5558 | -0.9971 | -0.6067 | -0.3709 | 0.1961 | -0.0035 | -0.7017 | 0.3771 | 0.6913 | 0.1639 | 0.0327 | 1.0305 | -0.3527 | 0.8231 | -42.4863 | 48.1688 | -35.1842 |
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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 2 through 164 )A2 - 164 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 165 through 340 )A165 - 340 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 341 through 476 )A341 - 476 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 2 through 176 )B2 - 176 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 177 through 288 )B177 - 288 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 289 through 315 )B289 - 315 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 316 through 476 )B316 - 476 | 8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 2 through 220 )C2 - 220 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 221 through 315 )C221 - 315 | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 316 through 475 )C316 - 475 | 11 | X-RAY DIFFRACTION | 11 | chain 'D' and (resid 2 through 202 )D2 - 202 | 12 | X-RAY DIFFRACTION | 12 | chain 'D' and (resid 203 through 290 )D203 - 290 | 13 | X-RAY DIFFRACTION | 13 | chain 'D' and (resid 291 through 475 )D | | | | | | | | | | | | | | | | | | | | | | | | | |
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