ソフトウェア | 名称 | バージョン | 分類 |
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XDS | | データ削減 | XSCALE | | データスケーリング | PHENIX | 1.18.2精密化 | PDB_EXTRACT | 3.25 | データ抽出 | PHASER | | 位相決定 | Coot | | モデル構築 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: NAD and P218-bound structure, PDB entry 6uww 解像度: 1.6→44.1 Å / SU ML: 0.1607 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 19.5376 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1915 | 2117 | 10.09 % | 0 |
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Rwork | 0.1605 | 18866 | - | - |
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obs | 0.1637 | 20983 | 95.01 % | - |
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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: 18.22 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→44.1 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1232 | 0 | 85 | 218 | 1535 |
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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_d0.0086 | 1440 | X-RAY DIFFRACTION | f_angle_d1.1306 | 1996 | X-RAY DIFFRACTION | f_chiral_restr0.0585 | 218 | X-RAY DIFFRACTION | f_plane_restr0.0088 | 271 | X-RAY DIFFRACTION | f_dihedral_angle_d21.2928 | 554 | | | | | |
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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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1.6-1.64 | 0.2611 | 103 | 0.2171 | 1050 | X-RAY DIFFRACTION | 79.63 | 1.64-1.68 | 0.2209 | 128 | 0.1842 | 1164 | X-RAY DIFFRACTION | 86.48 | 1.68-1.72 | 0.2037 | 120 | 0.1669 | 1156 | X-RAY DIFFRACTION | 89.36 | 1.72-1.77 | 0.2454 | 121 | 0.1713 | 1204 | X-RAY DIFFRACTION | 89.47 | 1.77-1.83 | 0.215 | 134 | 0.168 | 1207 | X-RAY DIFFRACTION | 91.29 | 1.83-1.9 | 0.2024 | 157 | 0.1708 | 1186 | X-RAY DIFFRACTION | 93.07 | 1.9-1.97 | 0.2121 | 137 | 0.1676 | 1315 | X-RAY DIFFRACTION | 98.17 | 1.97-2.06 | 0.2048 | 139 | 0.1659 | 1301 | X-RAY DIFFRACTION | 97.56 | 2.06-2.17 | 0.1785 | 160 | 0.1644 | 1315 | X-RAY DIFFRACTION | 100 | 2.17-2.31 | 0.2058 | 164 | 0.1648 | 1293 | X-RAY DIFFRACTION | 99.86 | 2.31-2.49 | 0.2148 | 159 | 0.1747 | 1315 | X-RAY DIFFRACTION | 100 | 2.49-2.74 | 0.1723 | 148 | 0.1641 | 1329 | X-RAY DIFFRACTION | 100 | 2.74-3.13 | 0.2251 | 141 | 0.1633 | 1341 | X-RAY DIFFRACTION | 100 | 3.13-3.94 | 0.1768 | 149 | 0.1472 | 1330 | X-RAY DIFFRACTION | 100 | 3.95-44.1 | 0.1489 | 157 | 0.1383 | 1360 | X-RAY DIFFRACTION | 99.93 |
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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 | 2.74563847789 | 0.172559235433 | -0.204873596643 | 3.16310405423 | 0.187549246502 | 2.25275193237 | -0.00498658194842 | -0.201381568446 | 0.0709005738213 | 0.158118462944 | -0.0142686963199 | -0.14051504819 | -0.211295438221 | 0.107243263609 | 0.0544454497364 | 0.0712998660614 | -0.020452025985 | -0.009324669053 | 0.0401848492294 | -0.0128108922213 | 0.0936900216727 | 4.90260081177 | 0.923030217855 | 16.0966573518 | 2 | 2.20343473671 | -0.826965741897 | -0.141018562611 | 2.03894000478 | 1.08364708077 | 1.72328762086 | -0.0805835337727 | -0.275013502921 | 0.291775350134 | -0.0544134115598 | -0.182290890381 | 0.269772716176 | -0.571580799874 | -0.334631043555 | 0.0147646806316 | 0.12722830248 | 0.022009030297 | -0.0201603949064 | 0.111047927622 | -0.0418883296522 | 0.127946893406 | -8.12104476632 | 1.89691109367 | 13.6713766646 | 3 | 2.87338187738 | -1.15230952031 | 0.550094512861 | 2.47108581394 | 0.0696380763608 | 2.68543169447 | -0.0479568713467 | -0.185388583783 | -0.118281514608 | 0.139118990999 | 0.0208072154275 | 0.0831182252482 | 0.0380796870666 | -0.119298642159 | 0.044248087107 | 0.0600390535827 | -0.0167910100118 | 0.0126326241019 | 0.0355906402523 | 0.0022674342606 | 0.0805232448298 | -3.22730117364 | -10.9564825476 | 13.0312895611 | 4 | 4.85107355993 | -0.876487787295 | -0.64221947687 | 3.07479097603 | 0.791776330038 | 2.02038603974 | -0.100965388434 | 0.266421810907 | -0.37509548061 | -0.180444617086 | -0.042575823926 | -0.185805229271 | 0.250807312891 | 0.0957384842124 | 0.101648031385 | 0.141555289781 | 0.0135545274967 | 0.0312092362866 | 0.0797591865833 | -0.0246789428665 | 0.144488855226 | 1.9922945797 | -17.8980824555 | 6.08026993628 | 5 | 2.00612593487 | -0.133101830995 | -1.19602763788 | 5.56679220151 | 2.65137429719 | 2.55172544038 | -0.0257554123188 | 0.477071958659 | -0.269369628573 | -0.954971805775 | -0.220968949556 | 0.491176821228 | -0.0143694640095 | -0.52844864875 | 0.207923001186 | 0.217307477396 | -0.0363454147089 | -0.0660452132094 | 0.176084211142 | -0.0292396836753 | 0.178239424757 | -2.74129338663 | -8.2324360655 | 0.283096348662 | 6 | 2.29798626341 | -1.19225861875 | -0.281474644224 | 2.54072165078 | 0.190169747538 | 1.77250642948 | 0.0488239116654 | 0.100860805954 | 0.0334472094339 | -0.0787116224034 | -0.142928044305 | -0.112979658117 | -0.175058724516 | 0.0803302940324 | 0.0710690635876 | 0.0790939601215 | -0.0232019984359 | -0.000318718707223 | 0.0493044601783 | 0.0159824311025 | 0.0890038443073 | 5.2571818768 | 0.976760154612 | 6.39612628442 | 7 | 6.06760606035 | -4.99747195597 | -1.97734354968 | 4.39227750348 | 1.92205834543 | 0.956118792089 | -0.207922152328 | -0.934069881491 | 0.855866278051 | 0.230734949594 | 0.672994301669 | -1.23632381857 | -0.144336653813 | 0.391688770745 | -0.478441725355 | 0.174326594416 | -0.00420036283611 | -0.0514875579114 | 0.277666050031 | -0.103360349898 | 0.288946406274 | 13.4382949892 | 1.50411780115 | 22.7451227248 | 8 | 0.0686728989173 | -0.157843475115 | 0.522529631261 | 1.12966737804 | -0.761091561475 | 4.16085310355 | 0.0512107790518 | 0.122184635238 | 0.245685839629 | -0.053771750189 | -0.172071916085 | -0.290936093341 | -0.549846395013 | 0.409615025948 | 0.0687411201839 | 0.164973356368 | -0.0366586267238 | 0.0305138679152 | 0.127321876762 | 0.0401957887618 | 0.156295316412 | 8.52498471379 | 8.01929852031 | 3.5357786786 | 9 | 1.72585022663 | -0.474459930442 | -2.50660645661 | 0.91777550869 | 1.25449497856 | 5.50579624854 | 0.11907351575 | 0.0210752504766 | 0.133358612822 | 0.195180450651 | -0.0861422729717 | -0.139192391818 | -0.254718857824 | -0.196007223643 | -0.0197626630973 | 0.26142387514 | 0.00948279000568 | -0.00187102855939 | 0.0847277136244 | -0.0172170427744 | 0.135482788477 | -0.477508363989 | 11.6552338728 | 12.2603621039 | 10 | 2.00000063148 | -5.75376752928 | -5.00030673688 | 2.00000090838 | 1.99999877796 | 2.00000039468 | 1.18488105133 | -0.401781056988 | 0.60479991709 | 5.04881704848 | -1.34579706422 | -0.672043516393 | 0.590218615965 | 0.674758906489 | 0.134098173267 | 0.643679487151 | -0.0359428152688 | -0.0588899396503 | 0.745158519487 | 0.0438597159685 | 0.623142410211 | 7.92180344859 | 10.6479800295 | 10.3239660058 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A ID | Refine TLS-ID | Selection details | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 3 through 26 )A3 - 26 | 1 - 24 | 2 | 2 | chain 'A' and (resid 27 through 37 )A27 - 37 | 25 - 35 | 3 | 3 | chain 'A' and (resid 38 through 62 )A38 - 62 | 36 - 60 | 4 | 4 | chain 'A' and (resid 63 through 87 )A63 - 87 | 61 - 85 | 5 | 5 | chain 'A' and (resid 88 through 102 )A88 - 102 | 86 - 100 | 6 | 6 | chain 'A' and (resid 103 through 122 )A103 - 122 | 101 - 120 | 7 | 7 | chain 'A' and (resid 123 through 132 )A123 - 132 | 121 - 130 | 8 | 8 | chain 'A' and (resid 133 through 145 )A133 - 145 | 131 - 143 | 9 | 9 | chain 'A' and (resid 146 through 165 )A146 - 165 | 144 - 163 | 10 | 10 | chain 'A' and (resid 301 through 301 )C301 | 2 | | | | | | | | | | | | | | | | | | | | |
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