ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.20.1_4487精密化 | autoPROC | 20211020 | data processingXDS | | データ削減 | Aimless | | データスケーリング | PHASER | | 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: 2VLH 解像度: 1.6→58.41 Å / SU ML: 0.2452 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 27.778 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 | 0.221 | 1985 | 0.94 % |
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Rwork | 0.1774 | 209779 | - |
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obs | 0.1778 | 211764 | 98.65 % |
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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: 35.33 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→58.41 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 14481 | 0 | 79 | 1529 | 16089 |
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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_d0.0137 | 15210 | X-RAY DIFFRACTION | f_angle_d1.2054 | 20561 | X-RAY DIFFRACTION | f_chiral_restr0.0651 | 2181 | X-RAY DIFFRACTION | f_plane_restr0.0127 | 2690 | X-RAY DIFFRACTION | f_dihedral_angle_d13.6438 | 5802 | | | | | |
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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 | 0.3573 | 134 | 0.3557 | 14213 | X-RAY DIFFRACTION | 93.39 | 1.64-1.68 | 0.3889 | 140 | 0.3337 | 14809 | X-RAY DIFFRACTION | 97.53 | 1.68-1.73 | 0.3296 | 141 | 0.3108 | 14823 | X-RAY DIFFRACTION | 97.86 | 1.73-1.79 | 0.2927 | 141 | 0.2864 | 14953 | X-RAY DIFFRACTION | 98.4 | 1.79-1.85 | 0.3577 | 141 | 0.266 | 14892 | X-RAY DIFFRACTION | 97.72 | 1.85-1.93 | 0.3007 | 144 | 0.2434 | 15143 | X-RAY DIFFRACTION | 99.75 | 1.93-2.02 | 0.2841 | 143 | 0.2295 | 15102 | X-RAY DIFFRACTION | 99.66 | 2.02-2.12 | 0.3055 | 143 | 0.214 | 15107 | X-RAY DIFFRACTION | 99.49 | 2.12-2.26 | 0.2446 | 143 | 0.1994 | 15128 | X-RAY DIFFRACTION | 99.34 | 2.26-2.43 | 0.2627 | 142 | 0.1914 | 15068 | X-RAY DIFFRACTION | 99.28 | 2.43-2.67 | 0.2219 | 143 | 0.1835 | 15087 | X-RAY DIFFRACTION | 99.42 | 2.67-3.06 | 0.2492 | 143 | 0.1683 | 15145 | X-RAY DIFFRACTION | 99.68 | 3.06-3.86 | 0.1759 | 143 | 0.1381 | 15143 | X-RAY DIFFRACTION | 99.78 | 3.86-58.41 | 0.1447 | 144 | 0.1264 | 15166 | X-RAY DIFFRACTION | 99.85 |
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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 | 1.03170442771 | -0.408001750006 | -0.147239948861 | 1.38135713739 | 0.117437222137 | 1.29373427843 | -0.0279304695882 | -0.159526894634 | -0.0666999664249 | 0.135071825651 | -0.0160333673153 | 0.392651200646 | -0.0520721904849 | -0.320884142561 | 0.00211791107824 | 0.175302281908 | 0.0138335231062 | 0.0344641808051 | 0.29290478865 | -0.00736527822646 | 0.306870982324 | -26.0362149249 | 29.2779207987 | -14.0571509722 | 2 | 0.651628322678 | -0.0592953031385 | 0.284750724724 | 1.50052742847 | -0.660086191169 | 0.795201654888 | -0.0732264721127 | -0.11005351958 | 0.11984067009 | 0.557441949353 | 0.00334167678794 | -0.211936755024 | -0.248729849587 | 0.0674561232262 | 0.0335948654791 | 0.32583693869 | -0.00803441705736 | -0.063811768402 | 0.236810754293 | -0.0149623804197 | 0.246158487132 | 1.79788131724 | 33.7888679391 | -6.90906004544 | 3 | 0.490387885263 | 0.0971890270217 | 0.19701671959 | 1.17799253247 | 0.4454639259 | 0.645913270255 | 0.0215637680366 | 0.0115244592704 | 0.0397678933459 | 0.107514643915 | -0.00801180028575 | -0.0863582030974 | -0.071085922933 | 0.109027964835 | 0.00209402322822 | 0.201490906235 | -0.0123465600588 | -0.00595570532843 | 0.222995179923 | 0.0125739855625 | 0.22617921167 | -1.55950858153 | 28.6354948701 | -15.2226942175 | 4 | 0.720014844799 | -0.111137723665 | -0.0324969114828 | 0.614872578074 | -0.676149905207 | 0.739689709714 | -0.267488371664 | -0.347958378909 | 0.492062893621 | 0.771967683756 | 0.298309291877 | -0.135946196305 | -0.298526530492 | 0.0338978862073 | 0.0768056686401 | 0.497183347199 | 0.117677422801 | -0.067301026333 | 0.300497606363 | -0.115690890494 | 0.352161313574 | -21.0237696874 | 41.7498424822 | -3.32179703926 | 5 | 0.748401322128 | 0.465695180217 | 0.115302346923 | 0.678253013668 | -0.270039853126 | 1.01457296636 | -0.531547907682 | -0.523128332927 | 0.35901761623 | 0.928608201249 | 0.380095868321 | 0.516040080894 | 0.453339364776 | 0.0548542120797 | -0.166589657807 | 0.773055922762 | 0.342107037721 | 0.177266577118 | 0.480934419365 | -0.125879485746 | 0.282933576282 | -28.0998688079 | 38.8386025442 | -2.48885860007 | 6 | 0.926930162645 | -0.462740401148 | 0.452955405676 | 0.968536606724 | -0.29803493886 | 0.99554197322 | -0.00683979964333 | 0.152552331185 | 0.0441351650891 | -0.123636939281 | -0.085145111266 | -0.453956809063 | 0.152936500099 | 0.273393499543 | 0.07186098638 | 0.321546754589 | 0.048013911133 | 0.0332656551619 | 0.251645910048 | 0.0258561268211 | 0.369915135546 | 0.960403762342 | -3.86436422688 | -16.7490977865 | 7 | 0.774155039662 | -0.000163602402776 | 0.100104499445 | 1.24775896751 | -0.520938541478 | 0.844680193746 | 0.0248072795604 | -0.290161609387 | -0.0727335579748 | 0.534834379015 | -0.0228545385292 | 0.0934855815042 | 0.0527083587825 | -0.0170179606679 | -0.0043285655022 | 0.510550435253 | -0.0195117907324 | 0.04007213221 | 0.340754004803 | 0.0188281436679 | 0.211865929529 | -12.6436472056 | 1.90115162727 | 7.85383187547 | 8 | 0.766329973591 | 0.0275817026137 | 0.0518840925358 | 0.583485999092 | -0.423766325817 | 0.744334040626 | 0.0136387389084 | -0.126818183074 | -0.0531081643068 | 0.379925843422 | 0.051939792786 | 0.128804808769 | 0.0311626479265 | -0.08479453136 | -0.0167088171058 | 0.353014589643 | -0.0139432099355 | 0.0244788581278 | 0.245418045181 | 0.0142562276456 | 0.205132527942 | -13.9424099349 | 3.36881190563 | -2.97579671233 | 9 | 1.28276882008 | -0.321640869843 | 0.10474505028 | 0.977375776051 | -0.672763548598 | 0.848718936942 | -0.0994011091542 | -0.136823364706 | 0.276060481825 | 0.246878171914 | -0.132491550168 | -0.700049713476 | 0.174704165896 | 0.399809740048 | 0.0732874467952 | 0.446501660027 | 0.063274301516 | -0.122189329152 | 0.367735302154 | 0.0509494456736 | 0.572550194382 | 10.8637809399 | -6.59762323523 | -4.12584109696 | 10 | 0.281291966364 | 0.132651169065 | 0.161826774657 | 0.528035701505 | -0.251058863393 | 1.27869528685 | -0.0694422331026 | 0.130121840302 | 0.0599653874377 | -0.134649117954 | -0.0473123214146 | -0.12851243093 | -0.15057188802 | 0.20182732567 | 0.0438347332725 | 0.223994199388 | -0.00253163524023 | 0.00426822348609 | 0.265020426149 | 0.0219592778878 | 0.29961429613 | -18.1869231257 | 26.8705458399 | -40.8239736977 | 11 | 0.56553409112 | -0.05146851718 | 0.196310133818 | 0.391375943506 | 0.131036126371 | 0.618820755236 | 0.00986344400455 | 0.0142704351394 | -0.0358670823489 | -0.0490471642356 | -0.0108473116738 | 0.0824960807838 | 0.025773141063 | -0.123940235783 | 0.00676021648344 | 0.167595606881 | -0.0109615904704 | 0.00190534050592 | 0.243695978882 | -0.0041955302642 | 0.247202048976 | -40.9189468414 | 13.3751129192 | -41.1161987823 | 12 | 0.801984932777 | -0.334043883928 | 0.0158487892176 | 0.905705511775 | 0.170054899323 | 0.884782305056 | 0.0104762018577 | 0.237081334933 | 0.0465628257359 | -0.300073020532 | -0.0541318345767 | -0.058826969253 | -0.200657140223 | 0.0087616614676 | 0.0229707266735 | 0.332098376437 | 0.00669793044648 | -0.0145331281938 | 0.266132007275 | 0.0247606523451 | 0.270520983218 | -26.7467261014 | 30.0908177679 | -53.7633211926 | 13 | 1.00751718902 | 0.568677941302 | 0.429753577386 | 1.02886911478 | 0.25733647902 | 0.564125250208 | 0.123214763006 | -0.142811489162 | -0.0558494245977 | 0.312606978278 | -0.111467764987 | 0.15470146915 | 0.249093793713 | -0.122892114954 | 0.00285404113954 | 0.393287249446 | -0.0207422345895 | 0.0265513914005 | 0.246239319988 | 0.0197714968851 | 0.305050140094 | -23.3706973347 | -12.9657589415 | -25.4538051621 | 14 | 0.546863002173 | -0.181192633679 | 0.140714284662 | 1.18445435952 | 0.365263542967 | 0.868227366856 | 0.0283441116618 | 0.109473811693 | -0.0778322541285 | -0.088035111613 | 0.00336577337018 | -0.0575874786971 | 0.140510252927 | 0.0719152967419 | -0.0178559085617 | 0.20469484527 | 0.0119808758178 | 0.00994336105194 | 0.213238781728 | -0.00914797612623 | 0.204754425499 | -11.7434379284 | -7.0774517555 | -48.3305412456 | 15 | 0.84395467649 | -0.226169056483 | -0.212285482468 | 0.871145222254 | -0.0124345478113 | 0.508554665276 | 0.00474730409346 | 0.144573905389 | -0.229980066538 | -0.0896809594158 | -0.00835338110611 | 0.214379203898 | 0.314302968038 | -0.0951007132211 | 0.0182691180052 | 0.443225743181 | -0.03403452715 | -0.0293577892222 | 0.244616915564 | -0.0219927009683 | 0.339973351347 | -24.1529737535 | -23.8756134129 | -38.3588880721 | 16 | 0.84683137685 | -0.163253012904 | 0.250401427371 | 0.547206986143 | 0.132747715406 | 0.460354944224 | -0.061978447749 | -0.0275122537791 | -0.231803347922 | 0.240456907077 | 0.0445816432997 | 0.231987458142 | 0.201531945331 | -0.193319401216 | 0.0281834248048 | 0.489260441086 | -0.0520855757191 | 0.0115195776387 | 0.288700824886 | -0.011800016004 | 0.397354772554 | -29.5122961905 | -23.4611466737 | -33.0759206591 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION ID | Refine TLS-ID | Selection details | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 1 through 57 )AA1 - 57 | 1 - 57 | 2 | 2 | chain 'A' and (resid 58 through 228 )AA58 - 228 | 58 - 228 | 3 | 3 | chain 'A' and (resid 229 through 331 )AA229 - 331 | 229 - 331 | 4 | 4 | chain 'A' and (resid 332 through 413 )AA332 - 413 | 332 - 413 | 5 | 5 | chain 'A' and (resid 414 through 456 )AA414 - 456 | 414 - 456 | 6 | 6 | chain 'B' and (resid 1 through 57 )BF1 - 57 | 1 - 57 | 7 | 7 | chain 'B' and (resid 58 through 271 )BF58 - 271 | 58 - 271 | 8 | 8 | chain 'B' and (resid 272 through 332 )BF272 - 332 | 272 - 332 | 9 | 9 | chain 'B' and (resid 333 through 456 )BF333 - 456 | 333 - 456 | 10 | 10 | chain 'C' and (resid 1 through 57 )CJ1 - 57 | 1 - 57 | 11 | 11 | chain 'C' and (resid 58 through 331 )CJ58 - 331 | 58 - 331 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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