ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.12_2829精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | MOLREP | | 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: 2xtp 解像度: 2.80038678769→39.0355231003 Å / SU ML: 0.367330651165 / 交差検証法: FREE R-VALUE / σ(F): 1.99501071312 / 位相誤差: 25.3287354556 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 |
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Rfree | 0.268149989389 | 309 | 4.6967624259 % |
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Rwork | 0.215153938036 | 6270 | - |
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obs | 0.217666000947 | 6579 | 99.0514905149 % |
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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 mean: 27.7779106911 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.80038678769→39.0355231003 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1872 | 0 | 29 | 14 | 1915 |
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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_d0.00391852906709 | 1966 | X-RAY DIFFRACTION | f_angle_d0.819341518661 | 2662 | X-RAY DIFFRACTION | f_chiral_restr0.0452000291228 | 294 | X-RAY DIFFRACTION | f_plane_restr0.0052578644946 | 346 | X-RAY DIFFRACTION | f_dihedral_angle_d14.2906145126 | 1630 | | | | | |
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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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2.8004-2.9004 | 0.389409300673 | 31 | 0.281011119735 | 595 | X-RAY DIFFRACTION | 95.865237366 | 2.9004-3.0165 | 0.414787683567 | 32 | 0.259735350036 | 603 | X-RAY DIFFRACTION | 98.9096573209 | 3.0165-3.1538 | 0.261874424713 | 23 | 0.226378875194 | 623 | X-RAY DIFFRACTION | 99.0797546012 | 3.1538-3.32 | 0.309648180709 | 29 | 0.224105775997 | 605 | X-RAY DIFFRACTION | 99.3730407524 | 3.32-3.5278 | 0.249402451446 | 27 | 0.230129136357 | 623 | X-RAY DIFFRACTION | 99.0853658537 | 3.5278-3.8 | 0.262066270501 | 29 | 0.202460228285 | 633 | X-RAY DIFFRACTION | 99.5488721805 | 3.8-4.182 | 0.283699716613 | 31 | 0.192669429453 | 631 | X-RAY DIFFRACTION | 99.6987951807 | 4.182-4.7862 | 0.219549530579 | 25 | 0.178472180032 | 635 | X-RAY DIFFRACTION | 100 | 4.7862-6.0266 | 0.27517024657 | 37 | 0.2055956971 | 641 | X-RAY DIFFRACTION | 99.5594713656 | 6.0266-39 | 0.204964808956 | 45 | 0.218593340949 | 681 | X-RAY DIFFRACTION | 99.316005472 |
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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 | 1.99718763149 | -0.45955894891 | -0.326395904436 | 1.96565076036 | -0.313227252424 | 3.76993722207 | 0.0736453931312 | 0.202625075066 | -0.545254118038 | -0.0311967522988 | -0.111608369656 | 0.223239453879 | 0.101731299695 | 0.0383393919046 | 0.0804478295307 | 0.0743948746959 | -0.0442330329362 | 0.0199916881337 | 0.111127672982 | -0.0647035802706 | 0.137525752058 | 16.1379746315 | -0.422525822387 | 20.2385783104 | 2 | 1.77797892228 | 0.48951618693 | -0.124451207338 | 2.43177184503 | -0.895232626099 | 0.708798998441 | 0.209185717421 | -0.12315650947 | -0.320216916275 | 0.106464149115 | -0.273329732431 | -0.110247976735 | -0.00955202579548 | 0.226887607501 | 0.105721181335 | 0.142905455349 | 0.0114459315262 | 0.00238510510979 | 0.165791898676 | 0.00663014105619 | 0.173488004479 | 20.2141514006 | 6.57250166985 | 19.5580336896 | 3 | 1.87981207491 | 0.456778682566 | 0.157300039555 | 1.59071453065 | 0.446358496694 | 1.15165963854 | -0.191180763323 | -0.187405773178 | 0.140694671683 | -0.145319953541 | 0.167451875697 | 0.342506740718 | 0.0860880259829 | -0.192664840347 | 0.00719508967531 | 0.102743157245 | 0.0345184767709 | -0.0507967005068 | 0.147109653483 | -0.00710745218811 | 0.207111509148 | 2.75454339488 | 6.902920245 | 17.1487922524 | 4 | 0.429886568363 | -0.13103850074 | 0.187474916512 | 1.52965768607 | -0.61401234901 | 0.746964462801 | -0.00102696141278 | 0.151502192848 | -0.150366847425 | -0.425615732191 | 0.0208177569036 | 0.14130366849 | 0.27795879194 | -0.0558660952753 | 0.0672162640118 | 0.241201090801 | -0.0538980489234 | 0.0402725604645 | 0.101814035596 | -0.0394013316317 | 0.343079842743 | 10.2106392732 | -0.308017283908 | 9.59591765612 | 5 | 5.4611201806 | 0.302142797792 | -1.7335529534 | 1.52349104547 | -0.195217836213 | 2.22024649237 | 0.621171096732 | 0.635224470785 | 0.797434031958 | -0.44995096772 | -0.427201969212 | 0.0189177323387 | -0.39677550111 | 0.274951436058 | -0.14162616604 | 0.467292343688 | -0.109496579689 | 0.0948274029776 | 0.261693019367 | 0.00551782412043 | 0.212091688371 | 24.1173541673 | 21.2541009413 | 9.56682699361 |
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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 27:56)2 | X-RAY DIFFRACTION | 2 | (chain A and resseq 57:108)3 | X-RAY DIFFRACTION | 3 | (chain A and resseq 109:180)4 | X-RAY DIFFRACTION | 4 | (chain A and resseq 181:231)5 | X-RAY DIFFRACTION | 5 | (chain A and resseq 232:263) | | | | |
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