ソフトウェア | 名称 | バージョン | 分類 |
---|
ADSC | Quantumデータ収集 | PHASER | | 位相決定 | PHENIX | (phenix.refine: dev_1005)精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | | |
|
---|
精密化 | 構造決定の手法: 分子置換 / 解像度: 2.08→36.13 Å / SU ML: 0.23 / σ(F): 1.37 / 位相誤差: 32.47 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.261 | 844 | 10 % |
---|
Rwork | 0.208 | - | - |
---|
obs | 0.213 | 8444 | 92.9 % |
---|
all | - | 8444 | - |
---|
|
---|
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 |
---|
原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -8.3775 Å2 | -0 Å2 | 0 Å2 |
---|
2- | - | 26.8988 Å2 | -0 Å2 |
---|
3- | - | - | -18.5213 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.08→36.13 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 1165 | 0 | 26 | 20 | 1211 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.006 | 1210 | X-RAY DIFFRACTION | f_angle_d0.974 | 1640 | X-RAY DIFFRACTION | f_dihedral_angle_d14.88 | 432 | X-RAY DIFFRACTION | f_chiral_restr0.06 | 186 | X-RAY DIFFRACTION | f_plane_restr0.004 | 206 | | | | | |
|
---|
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 (%) |
---|
2.0747-2.2047 | 0.3161 | 107 | 0.2548 | 954 | X-RAY DIFFRACTION | 72 | 2.2047-2.3749 | 0.3332 | 126 | 0.228 | 1150 | X-RAY DIFFRACTION | 86 | 2.3749-2.6138 | 0.222 | 148 | 0.2037 | 1322 | X-RAY DIFFRACTION | 98 | 2.6138-2.9919 | 0.1968 | 150 | 0.1998 | 1353 | X-RAY DIFFRACTION | 100 | 2.9919-3.7688 | 0.25 | 151 | 0.2025 | 1368 | X-RAY DIFFRACTION | 100 | 3.7688-36.1345 | 0.2778 | 162 | 0.2049 | 1453 | X-RAY DIFFRACTION | 100 |
|
---|
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 | 2.6679 | -0.9745 | -1.7022 | 5.7098 | -1.0831 | 1.6353 | 0.3361 | -0.1052 | 0.007 | 0.2631 | 0.2264 | -0.4326 | 0.0224 | 0.1848 | -0.5461 | 0.1689 | -0.0121 | 0.041 | 0.7557 | -0.0601 | 0.4399 | 5.3817 | 2.851 | 19.471 | 2 | 5.8978 | -3.5081 | -2.653 | 7.0492 | -3.4134 | 6.2108 | 0.1038 | 0.9119 | -0.3848 | -0.0371 | 0.0737 | -0.157 | -1.1387 | 0.28 | -0.1094 | 0.2209 | -0.018 | 0.0414 | 0.3793 | -0.0211 | 0.2033 | 2.9812 | 6.1327 | 18.0434 | 3 | 3.4933 | 0.4731 | -3.1845 | 6.0089 | -2.6578 | 3.7291 | -0.3925 | 1.4231 | 0.1238 | -1.0546 | -0.4426 | 1.5555 | 0.8459 | -1.1191 | 0.8525 | 0.4865 | -0.0952 | -0.1222 | 1.0817 | -0.0964 | 0.676 | 1.5416 | -4.2695 | 0.7334 | 4 | 2.7748 | -2.3067 | -2.1678 | 4.0445 | 3.1791 | 8.6522 | 0.4492 | 0.8704 | -0.1808 | -0.6048 | -0.6933 | 0.3174 | -0.7176 | -0.9674 | 0.2071 | 0.3887 | 0.0086 | -0.0472 | 0.6996 | 0.0263 | 0.3273 | -0.0363 | 7.709 | 13.8409 | 5 | 8.7423 | 5.2755 | 6.8336 | 3.371 | 4.742 | 7.4334 | -1.4377 | 0.7786 | -0.2265 | -0.7231 | 1.2487 | -0.4114 | -1.1343 | 0.9005 | 0.0172 | 0.5418 | -0.0849 | -0.0528 | 0.6813 | 0.0399 | 0.3886 | 5.5327 | 14.6542 | 36.0388 | 6 | 9.6193 | 3.7673 | -2.1205 | 2.1844 | 0.5333 | 6.4627 | 0.0489 | -0.2606 | 0.9627 | 0.3166 | -0.2679 | 0.3093 | -0.2565 | 0.3193 | 0.1702 | 0.2391 | 0.0093 | -0.0402 | 0.5859 | 0.0477 | 0.4071 | -0.501 | 7.1819 | 30.5053 | 7 | 8.4119 | 0.6459 | -0.9987 | 4.037 | 2.9706 | 8.9815 | -0.4597 | -1.1777 | 1.1053 | 0.4349 | -0.0275 | 1.26 | 0.5197 | -1.4653 | 0.3582 | 0.3013 | -0.0498 | -0.0532 | 0.9922 | -0.0201 | 0.4937 | -8.0597 | 2.0329 | 20.1202 | 8 | 4.4215 | -0.0305 | -1.6612 | 2.13 | -0.3639 | 1.8028 | -0.2495 | 0.1043 | -0.6791 | 0.0864 | 0.0889 | 0.5383 | 0.1651 | -0.1557 | 0.0367 | -0.3019 | 0.0449 | 0.1269 | 0.7654 | 0.031 | 0.3864 | 0.6686 | -4.2022 | 17.8114 | 9 | 5.2772 | -4.9156 | 1.7382 | 6.0867 | 0.6614 | 4.0265 | -0.0578 | -1.097 | -0.7916 | 1.0162 | 0.4202 | -1.5795 | 0.0183 | 0.8614 | -0.2311 | 0.3379 | -0.0681 | -0.1629 | 1.3396 | 0.4535 | 0.8951 | 13.7385 | -0.5659 | 21.6328 | 10 | 5.0229 | -2.5835 | -4.8685 | 1.7424 | 2.3543 | 4.7731 | 0.0971 | -0.6952 | 0.4587 | 0.3922 | 0.2313 | -0.1464 | -0.2618 | 0.9041 | -0.2454 | 0.423 | -0.1317 | 0.0087 | 1.3857 | 0.1904 | 0.4895 | 12.1716 | 3.4482 | 34.544 | 11 | 1.214 | -0.343 | -0.6072 | 1.4391 | 1.4516 | 3.8875 | -0.3854 | -0.1713 | -0.5056 | 0.0504 | -0.0393 | 0.4088 | 0.4422 | -0.0183 | 0.343 | 0.2186 | -0.0254 | 0.0551 | 0.5406 | 0.0554 | 0.4171 | 2.9573 | -4.438 | 24.6439 | 12 | 3.1147 | -2.1288 | 4.9559 | 7.2654 | -1.8397 | 8.3258 | -0.1587 | -0.1842 | -1.0211 | -0.0235 | 0.4937 | -0.3825 | 0.6444 | 0.7978 | -0.221 | 0.2312 | 0.0652 | 0.0321 | 0.8215 | -0.0004 | 0.4724 | 16.9152 | -2.779 | 9.8791 | 13 | 9.3026 | -5.1021 | -0.0746 | 4.0431 | -1.2435 | 1.3344 | 0.0561 | -0.2119 | 0.9984 | -0.1768 | 0.2768 | -0.0759 | -0.6203 | -0.1613 | 0.194 | 0.2073 | -0.0613 | 0.0063 | 0.9893 | -0.1534 | 0.6347 | 20.4965 | 3.1331 | 8.897 | 14 | 2.8168 | 4.2702 | 1.5877 | 6.5653 | 1.793 | 8.2483 | -0.2166 | 1.6494 | 0.4398 | -1.1207 | 0.3121 | -0.3195 | -0.5592 | 0.5533 | -0.0538 | 0.4411 | 0.1044 | 0.1198 | 0.7248 | 0.1128 | 0.3847 | 9.0723 | 6.892 | 4.1833 | 15 | 9.6313 | 1.1 | 0.5876 | 4.8057 | -5.2539 | 9.1364 | 0.3926 | -0.8077 | 0.7249 | 0.1905 | -0.0647 | 0.8543 | -2.5367 | 0.5932 | 0.0204 | 0.804 | 0.0411 | 0.0038 | 0.3527 | -0.077 | 0.5351 | 8.1537 | 13.5836 | 11.023 | 16 | 7.5119 | 2.4446 | -1.1191 | 4.6654 | -0.3291 | 3.4718 | 0.0537 | -0.1459 | -0.8878 | -0.2397 | 0.1202 | -1.0708 | 0.0026 | 0.5333 | -0.1435 | 0.1737 | 0.0272 | -0.011 | 0.6841 | -0.0432 | 0.2988 | 8.0814 | -0.6923 | 12.1809 | 17 | 6.0686 | -1.1252 | -0.3598 | 6.0967 | 5.3296 | 9.0843 | -0.7676 | 0.2932 | -1.495 | 0.4241 | 0.2791 | 0.246 | 2.3687 | 1.8743 | 0.5618 | 0.6717 | 0.2501 | 0.1889 | 0.7575 | -0.0472 | 1.0493 | 7.918 | -11.6039 | 12.7308 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
---|
1 | X-RAY DIFFRACTION | 1 | (chain A and resid 1:11)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 12:19)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 20:26)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 27:37)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 38:45)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 46:56)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 57:63)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 64:69)9 | X-RAY DIFFRACTION | 9 | (chain A and resid 70:80)10 | X-RAY DIFFRACTION | 10 | (chain A and resid 81:86)11 | X-RAY DIFFRACTION | 11 | (chain A and resid 87:107)12 | X-RAY DIFFRACTION | 12 | (chain A and resid 108:116)13 | X-RAY DIFFRACTION | 13 | (chain A and resid 117:125)14 | X-RAY DIFFRACTION | 14 | (chain A and resid 126:134)15 | X-RAY DIFFRACTION | 15 | (chain A and resid 135:143)16 | X-RAY DIFFRACTION | 16 | (chain A and resid 144:157)17 | X-RAY DIFFRACTION | 17 | (chain A and resid 158:166) | | | | | | | | | | | | | | | | |
|
---|