ソフトウェア | 名称 | バージョン | 分類 |
---|
SBC-Collect | | データ収集 | HKL-3000 | | データ収集 | HKL-3000 | | 位相決定 | MOLREP | | 位相決定 | PHENIX | (phenix.refine: 1.7_650)精密化 | HKL-3000 | | データ削減 | HKL-3000 | | 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: 2.35→40.65 Å / SU ML: 0.32 / Isotropic thermal model: mixed / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 33 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.283 | 842 | 5.03 % | random |
---|
Rwork | 0.208 | - | - | - |
---|
all | 0.212 | 16745 | - | - |
---|
obs | 0.212 | 16745 | 97.55 % | - |
---|
|
---|
溶媒の処理 | 減衰半径: 0.72 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 33.454 Å2 / ksol: 0.364 e/Å3 |
---|
原子変位パラメータ | Biso mean: 30.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.8486 Å2 | -0 Å2 | 10.8873 Å2 |
---|
2- | - | -7.2363 Å2 | -0 Å2 |
---|
3- | - | - | 8.0849 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.35→40.65 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 3369 | 0 | 70 | 170 | 3609 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.017 | 3570 | X-RAY DIFFRACTION | f_angle_d1.615 | 4857 | X-RAY DIFFRACTION | f_dihedral_angle_d16.859 | 1235 | X-RAY DIFFRACTION | f_chiral_restr0.125 | 531 | X-RAY DIFFRACTION | f_plane_restr0.011 | 636 | | | | | |
|
---|
LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection obs | % reflection obs (%) |
---|
2.35-2.4972 | 0.4055 | 124 | 0.2899 | 2321 | 2445 | 86 | 2.4972-2.69 | 0.3131 | 137 | 0.228 | 2704 | 2857 | 100 | 2.69-2.9606 | 0.3166 | 136 | 0.2061 | 2682 | 2818 | 100 | 2.9606-3.3889 | 0.2976 | 167 | 0.1965 | 2697 | 2864 | 100 | 3.3889-4.2689 | 0.2416 | 150 | 0.1715 | 2707 | 2857 | 100 | 4.2689-40.6561 | 0.2486 | 128 | 0.2167 | 2792 | 2920 | 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 | 0.035 | 0.0209 | -0.0208 | 0.0248 | -0.0458 | 0.178 | 0.0115 | -0.0062 | 0.0327 | 0.0432 | -0.0086 | 0.01 | -0.0305 | 0.0768 | 0.0961 | 0.0542 | -0.0123 | 0.0411 | 0.0117 | 0.0315 | -0.0524 | -0.279 | 10.9716 | 28.4679 | 2 | 0.0587 | 0.0194 | 0.0315 | 0.2537 | 0.0383 | 0.023 | -0.0499 | 0.0865 | -0.0357 | 0.044 | 0.0487 | -0.1184 | 0.0126 | 0.0573 | 0.0016 | 0.0747 | -0.0107 | 0.0052 | 0.0987 | -0.0075 | 0.0861 | 5.7136 | -3.2047 | 24.2806 | 3 | 0.0228 | 0.0128 | 0.042 | 0.1764 | -0.0339 | 0.1573 | -0.0536 | 0.0468 | -0.0624 | -0.0298 | -0.0137 | -0.1611 | -0.0105 | 0.0704 | -0.0412 | 0.0797 | -0.0168 | 0.0112 | 0.0495 | -0.0168 | 0.1096 | -7.9402 | -10.1212 | 19.3427 | 4 | 0.0873 | 0.0005 | 0.0839 | 0.0647 | -0.0469 | 0.1144 | -0.0393 | 0.0163 | 0.0193 | 0.0078 | -0.0398 | -0.0084 | 0.0572 | -0.0043 | -0.0865 | 0.0868 | -0.0466 | -0.0111 | 0.0327 | 0.0176 | 0.1581 | 26.2428 | -37.6942 | 5.2085 | 5 | 0.0008 | -0.0071 | 0.0053 | 0.0654 | -0.0569 | 0.0798 | -0.002 | 0.0207 | 0.0189 | -0.0188 | -0.0399 | -0.0702 | 0.0231 | 0.0573 | 0.0085 | 0.0759 | -0.0208 | 0.0498 | 0.1492 | -0.0417 | 0.1664 | 15.2215 | -33.6761 | 2.7654 | 6 | 0.2742 | 0.0039 | 0.0053 | 0.0128 | -0.008 | 0.0038 | -0.0086 | 0.0082 | -0.058 | -0.0146 | 0.0557 | -0.0687 | 0.0077 | 0.0196 | 0.0327 | 0.0453 | -0.0294 | 0.008 | 0.0774 | 0.0191 | 0.1765 | 22.8402 | -30.2538 | 10.0262 | 7 | 0.118 | 0.0866 | 0.0183 | 0.0691 | 0.0375 | 0.0805 | 0.0123 | -0.0078 | -0.0414 | -0.0029 | 0.0416 | -0.0298 | 0.016 | -0.0096 | 0.1446 | 0.0287 | 0.0088 | 0.0455 | 0.0436 | 0.0305 | 0.1303 | 20.9999 | -34.0129 | 14.7987 | 8 | 0.0535 | 0.0232 | -0.0467 | 0.019 | -0.0118 | 0.0591 | -0.0202 | 0.0134 | -0.0238 | 0.0201 | 0.0003 | 0.0433 | -0.003 | -0.0362 | -0.0633 | 0.0204 | 0.0008 | 0.0567 | 0.0514 | 0.0221 | 0.0926 | 13.5566 | -20.8284 | 20.2463 | 9 | 0.0121 | 0.0108 | -0.0324 | 0.0383 | -0.0507 | 0.1012 | -0.0023 | 0.0126 | 0.01 | -0.0414 | 0.0204 | 0.0169 | 0.0297 | -0.0453 | 0.1027 | 0.1108 | 0.0329 | -0.0825 | 0.1303 | -0.0881 | 0.1176 | 20.8143 | -15.057 | 15.3657 | 10 | 0.018 | 0.0043 | 0.0092 | 0.048 | 0.0223 | 0.0137 | -0.0061 | 0.0136 | -0.0249 | -0.0109 | 0.0147 | -0.0654 | 0.0217 | 0.005 | -0.0082 | 0.1986 | -0.0751 | 0.0638 | 0.0788 | -0.0376 | 0.1324 | 21.8664 | -19.0238 | 2.4605 | 11 | 0.0007 | -0.0079 | -0.0062 | 0.1106 | 0.049 | 0.0543 | 0.0035 | -0.0116 | 0.0015 | 0.0335 | -0.0101 | 0.0424 | 0.0215 | -0.0069 | 0.0246 | 0.1322 | -0.0521 | -0.0079 | 0.1012 | -0.0665 | 0.1239 | 10.616 | -11.7327 | 2.903 | 12 | 0.0861 | 0.0044 | -0.0645 | 0.1306 | 0.1018 | 0.134 | 0.0538 | -0.0307 | -0.0631 | -0.0027 | 0.064 | 0.104 | -0.011 | -0.0525 | 0.0839 | 0.1225 | -0.0236 | -0.0319 | 0.1015 | 0.0435 | 0.096 | 23.2447 | -19.9121 | -0.1922 | 13 | 0.1304 | 0.039 | 0.0712 | 0.1191 | 0.0445 | 0.0595 | 0.0168 | 0.0438 | 0.0074 | 0.0321 | 0.0135 | -0.0031 | -0.0175 | -0.0191 | -0.0052 | 0.1025 | 0.0347 | 0.0336 | 0.1187 | 0.032 | 0.1559 | 13.2971 | -9.961 | -4.1177 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
---|
1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resseq 44:118)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 119:215)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 216:270)4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resseq 45:57)5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resseq 58:70)6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resseq 71:94)7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resseq 95:137)8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq 138:166)9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 167:194)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 195:215)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 216:239)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 240:255)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 256:270) | | | | | | | | | | | | |
|
---|