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→44.27 Å / SU ML: 0.1368 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 17.4672 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 | 0.1784 | 2074 | 9.49 % | 0 |
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Rwork | 0.1464 | 19781 | - | - |
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obs | 0.1494 | 21855 | 98.63 % | - |
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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: 15.55 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→44.27 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 | 92 | 205 | 1529 |
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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_d0.0072 | 1425 | X-RAY DIFFRACTION | f_angle_d1.084 | 1969 | X-RAY DIFFRACTION | f_chiral_restr0.0581 | 217 | X-RAY DIFFRACTION | f_plane_restr0.01 | 268 | X-RAY DIFFRACTION | f_dihedral_angle_d13.5904 | 546 | | | | | |
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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 | 0.2551 | 122 | 0.2053 | 1252 | X-RAY DIFFRACTION | 94.63 | 1.64-1.68 | 0.2208 | 135 | 0.1798 | 1274 | X-RAY DIFFRACTION | 94.95 | 1.68-1.72 | 0.219 | 117 | 0.1676 | 1279 | X-RAY DIFFRACTION | 95.16 | 1.72-1.77 | 0.1968 | 144 | 0.1593 | 1299 | X-RAY DIFFRACTION | 98.03 | 1.77-1.83 | 0.1924 | 113 | 0.1506 | 1311 | X-RAY DIFFRACTION | 98 | 1.83-1.9 | 0.1654 | 141 | 0.149 | 1316 | X-RAY DIFFRACTION | 98.98 | 1.9-1.97 | 0.1957 | 172 | 0.142 | 1299 | X-RAY DIFFRACTION | 99.66 | 1.97-2.06 | 0.1537 | 124 | 0.1373 | 1386 | X-RAY DIFFRACTION | 100 | 2.06-2.17 | 0.1531 | 126 | 0.1389 | 1321 | X-RAY DIFFRACTION | 100 | 2.17-2.31 | 0.166 | 148 | 0.1443 | 1319 | X-RAY DIFFRACTION | 100 | 2.31-2.49 | 0.1954 | 150 | 0.1429 | 1337 | X-RAY DIFFRACTION | 99.93 | 2.49-2.74 | 0.1771 | 142 | 0.1459 | 1334 | X-RAY DIFFRACTION | 100 | 2.74-3.13 | 0.1724 | 157 | 0.147 | 1328 | X-RAY DIFFRACTION | 100 | 3.13-3.94 | 0.1662 | 159 | 0.1321 | 1331 | X-RAY DIFFRACTION | 100 | 3.95-44.27 | 0.1712 | 124 | 0.1449 | 1395 | X-RAY DIFFRACTION | 100 |
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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 | 2.78055404451 | -0.0478547672929 | 0.195710165339 | 2.92595795099 | -0.203185351852 | 3.34381322031 | 0.0573633615491 | -0.206339687659 | 0.0958057114998 | 0.103676182507 | -0.0267127704155 | -0.100712525234 | -0.0692665103194 | -0.00977462906644 | -0.0153503921658 | 0.0459573006089 | -0.00569581404069 | 0.00804476761752 | 0.0438007601257 | -0.0059470820304 | 0.065783592315 | 5.18804965196 | 1.81815805988 | 16.1283077721 | 2 | 3.29491929859 | -0.523957495708 | -0.0122643639328 | 4.42450950718 | 3.2798274404 | 4.63522873144 | 0.0728970396705 | -0.163082921276 | 0.187797253822 | -0.0927501783669 | -0.185743100918 | 0.232685180196 | -0.245321628355 | -0.0649907615034 | 0.0894311412195 | 0.0595563990217 | 0.00303836169961 | 0.00100435089926 | 0.0509493538441 | -0.0122474429597 | 0.0885009468837 | -7.91341795665 | 2.87319239703 | 13.5374747624 | 3 | 4.06838310235 | -1.25712664848 | 0.486362241409 | 2.693348463 | -0.694080446125 | 3.0054534564 | -0.0151098364777 | -0.0839921534131 | -0.0657984932181 | 0.0434013604897 | -0.0267399009161 | 0.0986303040908 | 0.0428076624658 | -0.0395018002896 | 0.0399056683397 | 0.0541714212324 | -0.0117119248612 | 0.00537321179929 | 0.0199128022747 | -0.0168214979919 | 0.052152124532 | -3.28636423202 | -10.1335724292 | 12.8667689008 | 4 | 4.33454446246 | -1.3857548596 | -0.721360234631 | 3.7245940039 | -0.266591965578 | 1.51023449656 | -0.207089563726 | 0.287916917257 | -0.411341673083 | 0.0156381041339 | -0.00739606916867 | -0.245475670161 | 0.254167706112 | -0.0617205176445 | 0.111873424203 | 0.120627583795 | 0.00975593568885 | 0.0275425485292 | 0.0527401712075 | -0.0338536644185 | 0.13353661025 | 0.988785139739 | -18.3742976266 | 8.80868348037 | 5 | 2.43391745978 | 0.314745734884 | -0.593965892568 | 7.19227979314 | 1.12268482792 | 3.97515508863 | 0.00269775105948 | 0.149209587714 | 0.280897676756 | -0.537172534459 | 0.123005872017 | -0.443948765599 | -0.0125589751452 | 0.313149776242 | 0.000594477460274 | 0.136260418696 | 0.0063203208402 | 0.0190706905284 | 0.124034464295 | -0.027133546483 | 0.111910102676 | 3.40942475309 | -15.1917356577 | 1.59061014083 | 6 | 0.576330751105 | 0.402521298341 | -0.636615382091 | 6.19250811113 | 2.52275180297 | 3.03126021068 | -0.234814741985 | 0.266554725309 | -0.292137847333 | -0.922000976114 | -0.028472897806 | 0.494011107336 | -0.261565048049 | -0.306944090126 | 0.0686550900401 | 0.197612911948 | -0.0225496521396 | -0.0502811880062 | 0.134384951853 | -0.0356211049647 | 0.165710238584 | -2.57098970664 | -7.54415306298 | 0.350396803164 | 7 | 3.39013868856 | -1.2835011726 | 1.17183773597 | 3.69405563166 | -2.73251475958 | 5.90041004735 | 0.144495118543 | 0.331699874531 | -0.0127925165075 | -0.303028558551 | -0.375843698747 | -0.0486187626303 | 0.0572655729003 | 0.294877648845 | 0.19505479522 | 0.0741693343485 | 0.0226888097518 | 0.0135353532755 | 0.0841095378924 | 0.00423715295994 | 0.0928627837534 | 9.04807105685 | -4.1773441871 | 4.16769559766 | 8 | 1.94190610756 | -1.58724512553 | -0.88609339014 | 2.70799830685 | 0.237563497524 | 0.389105474855 | -0.182117098414 | -0.183728345021 | 0.237805128437 | 0.158159585819 | 0.0954768064665 | -0.311456845129 | -0.131029000863 | -0.00921449137632 | 0.0547537129542 | 0.0784637626352 | -0.0209210357584 | -0.0238232558584 | 0.0440762922029 | -0.00688898729051 | 0.112785804343 | 7.21057018878 | 4.70887078303 | 14.6912206285 | 9 | 0.138418876128 | -0.234893943974 | 0.683181724594 | 1.01686104181 | -0.365513868294 | 3.15422322219 | 0.101441795236 | 0.222705484063 | 0.126998936055 | -0.0481823875531 | -0.193552352998 | -0.143055937641 | -0.508988872991 | 0.418810476781 | 0.0686284576523 | 0.139084284879 | -4.56840427273E-5 | 0.0357852237703 | 0.119533045428 | 0.0468796036764 | 0.124906575047 | 8.5811147371 | 8.72700319898 | 3.46077632865 | 10 | 2.04980492328 | -0.51395406028 | -3.06129686413 | 1.62967892122 | 2.51743084244 | 7.21846556132 | 0.107371699389 | 0.0888744433362 | 0.0953395430677 | -0.0878477680395 | -0.0924684712434 | -0.00696890977417 | -0.100525478017 | -0.203800584912 | -0.013566493221 | 0.123461398173 | 0.0152393220142 | 0.000505051909494 | 0.0503977601201 | 0.00456780548997 | 0.091608954004 | -0.101581269116 | 11.8661584442 | 10.9204890595 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A ID | Refine TLS-ID | Selection details | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 3 through 26 )3 - 26 | 1 - 24 | 2 | 2 | chain 'A' and (resid 27 through 37 )27 - 37 | 25 - 35 | 3 | 3 | chain 'A' and (resid 38 through 62 )38 - 62 | 36 - 60 | 4 | 4 | chain 'A' and (resid 63 through 78 )63 - 78 | 61 - 76 | 5 | 5 | chain 'A' and (resid 79 through 87 )79 - 87 | 77 - 85 | 6 | 6 | chain 'A' and (resid 88 through 102 )88 - 102 | 86 - 100 | 7 | 7 | chain 'A' and (resid 103 through 112 )103 - 112 | 101 - 110 | 8 | 8 | chain 'A' and (resid 113 through 132 )113 - 132 | 111 - 130 | 9 | 9 | chain 'A' and (resid 133 through 145 )133 - 145 | 131 - 143 | 10 | 10 | chain 'A' and (resid 146 through 165 )146 - 165 | 144 - 163 | | | | | | | | | | |
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