ソフトウェア | 名称 | バージョン | 分類 |
---|
REFMAC | 5.2.0019精密化 | ADSC | Quantumデータ収集 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | REFMAC | 5.2 | 位相決定 | | |
|
---|
精密化 | 構造決定の手法: フーリエ合成 開始モデル: PDB ENTRY 2G8Q 解像度: 1.6→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.895 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.099 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.21927 | 1557 | 5 % | RANDOM |
---|
Rwork | 0.18153 | - | - | - |
---|
obs | 0.18337 | 29458 | 98.39 % | - |
---|
all | - | 31015 | - | - |
---|
|
---|
溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK |
---|
原子変位パラメータ | Biso mean: 14.73 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.27 Å2 | 0 Å2 | 0.23 Å2 |
---|
2- | - | 0.2 Å2 | 0 Å2 |
---|
3- | - | - | 0.07 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.103 Å | 0.101 Å |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 1.6→30 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 1902 | 0 | 22 | 311 | 2235 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.009 | 0.022 | 1966 | X-RAY DIFFRACTION | r_angle_refined_deg1.242 | 1.942 | 2662 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.731 | 5 | 246 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.76 | 25.227 | 88 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg10.711 | 15 | 336 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg12.546 | 15 | 8 | X-RAY DIFFRACTION | r_chiral_restr0.085 | 0.2 | 295 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 1475 | X-RAY DIFFRACTION | r_nbd_refined0.19 | 0.2 | 912 | X-RAY DIFFRACTION | r_nbtor_refined0.294 | 0.2 | 1363 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.116 | 0.2 | 230 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.199 | 0.2 | 58 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.172 | 0.2 | 31 | X-RAY DIFFRACTION | r_mcbond_it0.658 | 1.5 | 1271 | X-RAY DIFFRACTION | r_mcangle_it1.099 | 2 | 2008 | X-RAY DIFFRACTION | r_scbond_it1.693 | 3 | 776 | X-RAY DIFFRACTION | r_scangle_it2.663 | 4.5 | 654 | | | | | | | | | | | | | | | | | |
|
---|
LS精密化 シェル | 解像度: 1.6→1.643 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.264 | 114 | - |
---|
Rwork | 0.205 | 2069 | - |
---|
obs | - | - | 94.42 % |
---|
|
---|
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) |
---|
1 | 14.4672 | -0.2242 | 2.344 | 4.5506 | 9.0359 | 18.48 | -0.0536 | 0.2333 | 0.843 | -1.0543 | 0.6884 | -0.3994 | -2.2541 | 0.7331 | -0.6348 | 0.2928 | -0.1172 | 0.0925 | -0.0698 | -0.0057 | -0.013 | 33.1603 | 15.1262 | 11.8441 | 2 | 3.5095 | -0.8096 | -0.4141 | 4.2051 | 0.8024 | 6.3631 | 0.081 | 0.1881 | -0.0343 | -0.1743 | -0.0301 | -0.1111 | -0.2513 | -0.071 | -0.0509 | 0.0604 | -0.0004 | 0.0202 | 0.0285 | 0.0122 | -0.0036 | 29.2759 | 5.7692 | 7.7001 | 3 | 14.4841 | -11.5597 | -15.2576 | 19.3742 | 10.647 | 39.8524 | -0.3698 | 0.6555 | -0.3615 | 1.2094 | 0.3749 | 1.1041 | 0.3855 | -3.4959 | -0.0051 | 0.0123 | 0.0189 | 0.0495 | 0.3025 | 0.0372 | -0.0622 | 24.6546 | -5.1796 | -1.8714 | 4 | 4.9798 | 2.2467 | -0.4125 | 9.2695 | 4.7436 | 6.0274 | 0.0216 | 0.633 | -0.0239 | -0.6791 | -0.0165 | 0.0323 | -0.3749 | -0.1009 | -0.0051 | 0.0431 | 0.0119 | 0.0309 | 0.1018 | -0.0307 | -0.0527 | 33.7669 | 0.1868 | -2.99 | 5 | 44.8303 | -9.9178 | -4.3925 | 6.7113 | 2.4179 | 2.0465 | -0.0695 | -0.9374 | 1.0342 | -0.2762 | 0.4718 | -1.1047 | -0.4309 | 0.3442 | -0.4023 | 0.0031 | -0.074 | 0.0933 | 0.0168 | -0.0565 | 0.0886 | 40.5769 | 6.3477 | 2.5273 | 6 | 1.6244 | 0.0032 | -1.9239 | 0.9795 | 0.5032 | 3.4466 | -0.0635 | 0.0116 | -0.0766 | -0.1109 | 0.0665 | -0.0448 | -0.1051 | 0.0143 | -0.003 | 0.0313 | 0 | 0.002 | 0.0427 | 0.0064 | 0.0156 | 27.4469 | 1.1557 | 10.3736 | 7 | 5.2829 | 0.357 | 1.1887 | 1.0312 | -0.214 | 2.4311 | 0.0005 | -0.0144 | -0.1016 | 0.0226 | 0.02 | -0.0818 | -0.044 | -0.1217 | -0.0205 | 0.0338 | 0.0039 | -0.0004 | 0.0305 | 0.0077 | 0.0344 | 28.4138 | -1.8143 | 24.0593 | 8 | 9.5375 | 1.6068 | -5.0634 | 1.0522 | -0.8421 | 4.1963 | -0.2741 | 0.0714 | -0.4231 | -0.2416 | 0.1216 | -0.3559 | 0.3263 | 0.2415 | 0.1526 | 0.0346 | -0.0001 | 0.058 | 0.0267 | -0.0543 | 0.0593 | 38.3818 | -4.6478 | 2.0918 | 9 | 2.0457 | 0.9448 | -2.3502 | 0.9358 | -0.338 | 3.8186 | -0.1827 | 0.1025 | -0.3749 | -0.0977 | 0.0604 | -0.191 | 0.3464 | -0.0357 | 0.1224 | 0.04 | -0.008 | 0.0112 | 0.026 | -0.0335 | 0.0275 | 30.0729 | -8.0598 | 6.2876 | 10 | 1.7291 | -0.3511 | 0.0282 | 4.0257 | 0.4828 | 2.1521 | -0.0382 | -0.0236 | 0.0827 | -0.057 | 0.062 | -0.0227 | -0.0791 | -0.1259 | -0.0238 | 0.0339 | 0.0088 | -0.0015 | 0.0252 | 0.0042 | 0.03 | 29.5699 | 3.9029 | 19.1805 | 11 | 4.0384 | 0.2409 | 1.1434 | 2.0898 | -0.1712 | 4.818 | 0.0131 | 0.1486 | -0.1992 | 0.1236 | 0.1653 | -0.0586 | 0.1804 | 0.0537 | -0.1784 | 0.0163 | 0.0035 | -0.0016 | 0.0368 | -0.0074 | 0.0337 | 16.1774 | -4.9416 | 30.3592 | 12 | 81.3737 | -17.5725 | 28.3624 | 5.8275 | -8.1429 | 11.8892 | -0.7946 | -1.9839 | 5.3744 | 0.0064 | 0.1121 | -0.5497 | -1.0954 | -0.0432 | 0.6825 | 0.2454 | -0.0425 | 0.0421 | 0.2869 | -0.0721 | 0.3066 | 10.9656 | 10.9049 | 21.8625 | 13 | 6.9683 | -4.6126 | 0.746 | 11.843 | -1.4918 | 0.1932 | 0.2576 | 0.8589 | -0.0642 | -1.0917 | -0.4102 | 0.1556 | -0.0448 | 0.1191 | 0.1526 | 0.0779 | 0.0139 | -0.0084 | 0.1237 | 0.0058 | -0.0912 | 9.8738 | -0.9694 | 19.2951 | 14 | 2.8973 | 2.1907 | -2.7751 | 11.4915 | 12.5581 | 45.2922 | 0.2279 | 0.1264 | -1.4126 | 0.5553 | 0.2249 | -0.2365 | 3.1268 | 1.0019 | -0.4527 | 0.1346 | 0.0881 | -0.0739 | -0.0242 | -0.0918 | 0.1606 | 5.3904 | -10.8507 | 21.3982 | 15 | 1.3009 | -0.1851 | 0.8861 | 1.3862 | 1.0912 | 1.6933 | -0.0483 | 0.1258 | 0.0378 | -0.0967 | 0.0484 | 0.0246 | -0.0675 | 0.0313 | -0.0001 | 0.0116 | -0.013 | 0.0061 | 0.0202 | 0.0152 | 0.0275 | 13.5222 | 3.5931 | 33.4997 | 16 | 6.7206 | 4.7668 | 0.7284 | 9.4315 | 2.2192 | 0.5581 | -0.1 | -0.17 | -0.2975 | 0.1352 | 0.0988 | 0.3401 | 0.1573 | -0.0904 | 0.0011 | 0.0145 | -0.0121 | 0.008 | 0.0218 | 0.0471 | 0.0453 | 7.7994 | -2.4987 | 46.6774 | 17 | 0.7267 | 0.4124 | -0.0783 | 0.6856 | 0.5461 | 0.7806 | -0.0417 | 0.045 | 0.0383 | -0.0691 | -0.0228 | 0.0576 | -0.0626 | -0.0531 | 0.0644 | 0.0183 | 0.0083 | -0.0176 | 0.0089 | 0.0068 | 0.0462 | 9.1908 | 5.5141 | 38.7281 | 18 | 5.6556 | -5.4373 | -2.8623 | 7.3882 | 6.0166 | 10.3505 | 0.2376 | 0.9221 | -0.6281 | -0.6665 | -0.4648 | 0.5656 | 0.4603 | -0.6327 | 0.2272 | 0.0549 | -0.0175 | -0.0626 | 0.0465 | -0.1117 | 0.0286 | -1.2997 | -5.2757 | 17.1666 | 19 | 1.6325 | 0.7242 | 2.2544 | 1.5546 | 1.9114 | 5.6282 | -0.1633 | 0.0944 | 0.0655 | -0.2297 | 0.0157 | 0.1802 | -0.4442 | -0.1598 | 0.1476 | 0.0338 | 0.0073 | -0.045 | 0.0303 | 0.021 | 0.046 | 3.9433 | 7.2694 | 29.0816 | 20 | 4.8151 | -1.8145 | 0.7759 | 2.0024 | -0.9905 | 3.0855 | -0.0285 | 0.0376 | -0.1081 | -0.0721 | -0.0171 | 0.1069 | 0.0767 | 0.0413 | 0.0456 | 0.0478 | -0.0141 | -0.0061 | 0.009 | 0.0028 | 0.0485 | 13.0433 | -2.8637 | 40.345 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | AA1 - 6 | 1 - 6 | 2 | X-RAY DIFFRACTION | 2 | AA7 - 16 | 7 - 16 | 3 | X-RAY DIFFRACTION | 3 | AA17 - 23 | 17 - 23 | 4 | X-RAY DIFFRACTION | 4 | AA24 - 32 | 24 - 32 | 5 | X-RAY DIFFRACTION | 5 | AA33 - 39 | 33 - 39 | 6 | X-RAY DIFFRACTION | 6 | AA40 - 58 | 40 - 58 | 7 | X-RAY DIFFRACTION | 7 | AA59 - 77 | 59 - 77 | 8 | X-RAY DIFFRACTION | 8 | AA78 - 95 | 78 - 95 | 9 | X-RAY DIFFRACTION | 9 | AA96 - 106 | 96 - 106 | 10 | X-RAY DIFFRACTION | 10 | AA107 - 124 | 107 - 124 | 11 | X-RAY DIFFRACTION | 11 | BB1 - 15 | 1 - 15 | 12 | X-RAY DIFFRACTION | 12 | BB16 - 23 | 16 - 23 | 13 | X-RAY DIFFRACTION | 13 | BB24 - 36 | 24 - 36 | 14 | X-RAY DIFFRACTION | 14 | BB37 - 41 | 37 - 41 | 15 | X-RAY DIFFRACTION | 15 | BB42 - 58 | 42 - 58 | 16 | X-RAY DIFFRACTION | 16 | BB59 - 70 | 59 - 70 | 17 | X-RAY DIFFRACTION | 17 | BB71 - 84 | 71 - 84 | 18 | X-RAY DIFFRACTION | 18 | BB85 - 96 | 85 - 96 | 19 | X-RAY DIFFRACTION | 19 | BB97 - 106 | 97 - 106 | 20 | X-RAY DIFFRACTION | 20 | BB107 - 124 | 107 - 124 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|