ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | PHENIX | 1.17.1_3660精密化 | SCALEPACK | | データスケーリング | PDB_EXTRACT | 3.25 | データ抽出 | HKL-3000 | | データ削減 | HKL-3000 | | 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: 6wa7 解像度: 1.4→48.67 Å / SU ML: 0.1206 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 16.9979 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 | 0.1807 | 12903 | 4.99 % |
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Rwork | 0.163 | - | - |
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obs | 0.1638 | 133136 | 96.57 % |
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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: 23.36 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.4→48.67 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5610 | 0 | 88 | 425 | 6123 |
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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_d0.0057 | 5999 | X-RAY DIFFRACTION | f_angle_d0.8704 | 8199 | X-RAY DIFFRACTION | f_chiral_restr0.0811 | 884 | X-RAY DIFFRACTION | f_plane_restr0.0057 | 1064 | X-RAY DIFFRACTION | f_dihedral_angle_d13.9735 | 2203 | | | | | |
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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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1.4-1.41 | 0.2718 | 382 | 0.2168 | 7273 | X-RAY DIFFRACTION | 85.81 | 1.41-1.43 | 0.212 | 419 | 0.2002 | 8043 | X-RAY DIFFRACTION | 95.72 | 1.43-1.45 | 0.216 | 516 | 0.1979 | 8130 | X-RAY DIFFRACTION | 95.45 | 1.45-1.47 | 0.2135 | 461 | 0.1917 | 8140 | X-RAY DIFFRACTION | 97.08 | 1.47-1.49 | 0.1966 | 425 | 0.1839 | 8166 | X-RAY DIFFRACTION | 95.61 | 1.49-1.51 | 0.2061 | 435 | 0.1759 | 8176 | X-RAY DIFFRACTION | 96.67 | 1.51-1.53 | 0.1869 | 474 | 0.1695 | 8173 | X-RAY DIFFRACTION | 96.89 | 1.53-1.55 | 0.1857 | 395 | 0.1627 | 8185 | X-RAY DIFFRACTION | 96.05 | 1.55-1.57 | 0.2001 | 439 | 0.1667 | 8021 | X-RAY DIFFRACTION | 95.1 | 1.57-1.6 | 0.1802 | 487 | 0.1581 | 8088 | X-RAY DIFFRACTION | 94.69 | 1.6-1.63 | 0.1838 | 397 | 0.159 | 8231 | X-RAY DIFFRACTION | 98.15 | 1.63-1.66 | 0.2112 | 403 | 0.1577 | 8224 | X-RAY DIFFRACTION | 96.07 | 1.66-1.69 | 0.1815 | 427 | 0.1558 | 8296 | X-RAY DIFFRACTION | 97.77 | 1.69-1.72 | 0.1964 | 420 | 0.1574 | 8245 | X-RAY DIFFRACTION | 96.93 | 1.72-1.76 | 0.1554 | 402 | 0.1513 | 8406 | X-RAY DIFFRACTION | 98.23 | 1.76-1.8 | 0.1781 | 403 | 0.1588 | 8204 | X-RAY DIFFRACTION | 96.83 | 1.8-1.85 | 0.1745 | 380 | 0.1596 | 8264 | X-RAY DIFFRACTION | 96.67 | 1.85-1.9 | 0.2015 | 444 | 0.1629 | 7980 | X-RAY DIFFRACTION | 94.64 | 1.9-1.95 | 0.1836 | 412 | 0.1612 | 8299 | X-RAY DIFFRACTION | 97.72 | 1.95-2.02 | 0.1782 | 452 | 0.1626 | 8300 | X-RAY DIFFRACTION | 97.21 | 2.02-2.09 | 0.1756 | 426 | 0.1636 | 8352 | X-RAY DIFFRACTION | 98.58 | 2.09-2.17 | 0.1829 | 472 | 0.1635 | 8258 | X-RAY DIFFRACTION | 98.22 | 2.17-2.27 | 0.1906 | 449 | 0.1614 | 8348 | X-RAY DIFFRACTION | 98.35 | 2.27-2.39 | 0.1832 | 395 | 0.1682 | 8134 | X-RAY DIFFRACTION | 95.53 | 2.39-2.54 | 0.1739 | 427 | 0.1645 | 8365 | X-RAY DIFFRACTION | 98.44 | 2.54-2.74 | 0.1795 | 444 | 0.1756 | 8429 | X-RAY DIFFRACTION | 98.86 | 2.74-3.01 | 0.1937 | 429 | 0.1749 | 8356 | X-RAY DIFFRACTION | 98.85 | 3.01-3.45 | 0.1853 | 425 | 0.1721 | 8191 | X-RAY DIFFRACTION | 96.55 | 3.45-4.34 | 0.172 | 436 | 0.1508 | 8299 | X-RAY DIFFRACTION | 97.52 | 4.34-48.67 | 0.1546 | 427 | 0.1464 | 8243 | X-RAY DIFFRACTION | 97 |
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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 | 0.253116794927 | 0.17503524487 | -0.00123080140912 | 0.395369604785 | 0.0318159152339 | 0.0320736455643 | -0.137785848818 | 0.362070684608 | 0.0988020059486 | -0.517543739709 | 0.066984099839 | 0.0631054110632 | -0.548426215358 | -0.100497284389 | -0.0135597090507 | 0.364019834917 | 0.0840273360419 | -0.0961729364564 | 0.226212020211 | 0.0534242830339 | 0.182472119451 | 24.2451695374 | 14.2936756997 | 13.7914937754 | 2 | 0.231557603777 | 0.143515375959 | 0.236433879356 | 0.547175411761 | 0.163692047048 | 0.267000263408 | -0.0137135675675 | 0.0421947052279 | -0.0233628347022 | -0.0717414843792 | -0.0461752301703 | 0.128887182151 | -0.0701436687595 | -0.197804919398 | -0.0280533649806 | 0.127281202665 | 0.0149275951938 | -0.0156599090035 | 0.177538118003 | -0.0421214194156 | 0.132768955216 | 21.2490869668 | 0.672774806677 | 21.4583815562 | 3 | 0.536162790472 | -0.0073165087872 | 0.15937893119 | 0.602447025797 | 0.00448600407686 | 0.214234587033 | 0.0215418051524 | -0.0870120992395 | -0.0892769131683 | 0.221478292364 | -0.00817981713082 | -0.0861080959389 | 0.140440530399 | -0.0335023923595 | -0.00411665939401 | 0.209724507764 | -0.0244762348793 | -0.0238882709376 | 0.115546867063 | 0.00969049643785 | 0.133863448572 | 36.481997557 | -10.8957831706 | 44.308408784 | 4 | 0.278952538345 | 0.16639318306 | -0.007966436662 | 0.470137667775 | 0.0398669335689 | 0.740322236559 | 0.0107183103219 | 0.0531314823142 | -0.084113103361 | -0.018839801369 | -0.0385006412899 | 0.129044532215 | 0.16899721077 | -0.171119791397 | -0.0194804823804 | 0.109659909216 | -0.0334278853724 | -0.00478488749985 | 0.145457313331 | -0.0416918412091 | 0.129516092642 | 20.9378941646 | -7.93234653285 | 27.7147303908 | 5 | 0.495305719053 | -0.0284382491454 | 0.226909197372 | 0.648265035031 | 0.0237266424421 | 0.828131853131 | -0.037139375938 | -0.000537313618047 | 0.0634476867342 | 0.0449907287936 | -0.054121672429 | 0.0451774767975 | -0.0956008393938 | -0.0928994875823 | -0.192853956341 | 0.100458882441 | 0.0012102358961 | -0.00254114442058 | 0.0911928895759 | -0.0254013600715 | 0.1153340752 | 28.4880304311 | 8.4601479677 | 33.8982126298 | 6 | 0.108022259058 | -0.0129046550655 | 0.00373046220721 | 0.107163024696 | -0.0839386363968 | 0.193000592446 | 0.0130032232933 | 0.164066366731 | -0.188538143981 | -0.443433250323 | -0.0522205582655 | 0.0495982275816 | 0.533942272083 | -0.0360507658609 | 0.0109432194179 | 0.457918812379 | 0.0129981807412 | 0.0528393493184 | 0.186741482621 | -0.011977212692 | 0.225338860804 | 67.48247805 | -9.80710242984 | 4.05455222059 | 7 | 0.826025695238 | 0.132917807752 | -0.535596046399 | 0.511203873833 | -0.222460702157 | 0.345147423708 | 0.0157915591241 | 0.0188126255032 | 0.0969050462272 | -0.197277141999 | -0.00336445408651 | -0.140746003875 | 0.105279641758 | 0.0316821320177 | 0.0065491775404 | 0.186440301264 | 0.00408810302539 | 0.0259555572011 | 0.149913959728 | 0.0311100864699 | 0.137596048368 | 69.0904567435 | 5.27452078051 | 9.23853736573 | 8 | 0.470000272346 | -0.0693606963562 | -0.490941323978 | 0.614435063597 | -0.0994861652209 | 0.487706916164 | 0.0919241790056 | -0.142476043043 | 0.176585644616 | 0.0972886425282 | 0.0626463796641 | 0.0917280276351 | -0.195512917499 | 0.212046207482 | 0.0527078321112 | 0.172312722332 | -0.0406947353236 | 0.0334379051811 | 0.152444208837 | -0.0290232690099 | 0.193246075165 | 56.3203729119 | 17.5108567373 | 33.4909651744 | 9 | 0.64961894074 | 0.0231775135614 | -0.648853062399 | 0.730733662566 | -0.0499419978776 | 0.847549786546 | 0.12256160275 | -0.111248423552 | 0.258175883158 | -0.215914994616 | 0.0415381729344 | -0.220499058771 | -0.160563784933 | 0.164661979303 | 0.0878111083556 | 0.141167850627 | -0.0410881455321 | 0.0315787534919 | 0.180870075447 | -0.00261188626226 | 0.210698404331 | 70.8315007714 | 13.8206267753 | 16.7052525791 | 10 | 0.58133493183 | 0.00193778125642 | -0.613401652329 | 0.631755040231 | 0.124541562876 | 0.716438521457 | -0.115792849614 | -0.11169777498 | -0.0839812305338 | -0.0551313798608 | 0.0229203906918 | -0.0387802896193 | 0.175542190631 | 0.102753624573 | -0.124634271352 | 0.126463058663 | 0.0064626945797 | 0.00436410541809 | 0.132139949834 | 0.0399797867367 | 0.127384315155 | 63.9310484862 | -3.07372966854 | 23.3548767309 |
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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 (resid 30 through 50 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 51 through 106 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 107 through 189 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 190 through 265 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 266 through 388 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 30 through 50 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 51 through 106 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 107 through 189 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 190 through 282 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 283 through 388 ) | | | | | | | | | |
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