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 | | 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: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.013 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.096 / 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 | 0.20937 | 1562 | 5 % | RANDOM |
---|
Rwork | 0.17861 | - | - | - |
---|
obs | 0.18016 | 29373 | 98.93 % | - |
---|
all | - | 31270 | - | - |
---|
|
---|
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: 16.207 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.08 Å2 | 0 Å2 | -0.03 Å2 |
---|
2- | - | 0.48 Å2 | 0 Å2 |
---|
3- | - | - | -0.4 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.096 Å | 0.099 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 | 48 | 369 | 2319 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.008 | 0.021 | 1999 | X-RAY DIFFRACTION | r_angle_refined_deg1.443 | 1.951 | 2708 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.593 | 5 | 246 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.14 | 25.169 | 89 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg10.404 | 15 | 339 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg11.274 | 15 | 8 | X-RAY DIFFRACTION | r_chiral_restr0.145 | 0.2 | 298 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 1505 | X-RAY DIFFRACTION | r_nbd_refined0.186 | 0.2 | 947 | X-RAY DIFFRACTION | r_nbtor_refined0.295 | 0.2 | 1374 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.127 | 0.2 | 305 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.165 | 0.2 | 67 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.106 | 0.2 | 45 | X-RAY DIFFRACTION | r_mcbond_it0.513 | 1.5 | 1273 | X-RAY DIFFRACTION | r_mcangle_it0.879 | 2 | 2022 | X-RAY DIFFRACTION | r_scbond_it1.319 | 3 | 801 | X-RAY DIFFRACTION | r_scangle_it2.158 | 4.5 | 686 | | | | | | | | | | | | | | | | | |
|
---|
LS精密化 シェル | 解像度: 1.6→1.641 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.254 | 120 | - |
---|
Rwork | 0.206 | 2120 | - |
---|
obs | - | - | 97.82 % |
---|
|
---|
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 | 16.0026 | 2.4745 | 1.0572 | 15.0953 | 7.5705 | 10.2913 | -0.0649 | -0.0451 | 0.7748 | -0.6494 | 0.3206 | -0.3655 | -1.7691 | 0.4812 | -0.2557 | 0.2667 | -0.0974 | 0.0794 | -0.067 | 0.03 | -0.0201 | 33.0819 | 15.1759 | 12.3871 | 2 | 3.5296 | -0.6955 | -0.0077 | 3.8318 | 1.0515 | 6.1276 | 0.1723 | 0.2198 | 0.0424 | -0.1098 | -0.032 | -0.0573 | -0.201 | -0.1292 | -0.1403 | 0.0546 | 0.0075 | 0.0242 | 0.0453 | 0.0426 | 0.0061 | 29.2271 | 5.7837 | 7.7378 | 3 | 3.1845 | -0.2125 | 2.744 | 0.0142 | -0.1831 | 2.3644 | 0.9789 | 0.4569 | -0.3852 | -0.2775 | -0.2313 | 0.8536 | -0.6267 | -0.7451 | -0.7476 | 0.513 | -0.0768 | 0.0269 | 0.3059 | -0.0798 | 0.1921 | 24.8214 | -5.2553 | -1.6926 | 4 | 3.4927 | -0.4901 | -2.344 | 0.8904 | 0.3491 | 2.9095 | 0.1008 | 0.2882 | 0.0765 | -0.1654 | 0.0634 | -0.1237 | -0.1339 | -0.0861 | -0.1642 | 0.0363 | -0.009 | 0.0118 | 0.0637 | 0.0106 | 0.0105 | 32.2213 | 2.1093 | 4.7363 | 5 | 4.1993 | 0.0597 | 0.6925 | 1.968 | -0.6101 | 2.1543 | -0.0306 | -0.0319 | -0.0719 | 0.1033 | 0.048 | -0.0849 | -0.0302 | -0.1844 | -0.0174 | 0.0494 | -0.0013 | -0.0001 | 0.0397 | 0.0081 | 0.0396 | 27.9791 | -1.6206 | 24.0285 | 6 | 11.0821 | 1.5675 | -5.5984 | 0.2988 | -1.1595 | 4.5813 | -0.2738 | 0.2381 | -0.4013 | -0.1508 | 0.1297 | -0.181 | 0.4579 | 0.0819 | 0.1442 | 0.0555 | -0.0178 | 0.0316 | 0.0278 | -0.0642 | 0.0202 | 38.4471 | -4.457 | 2.0132 | 7 | 8.7673 | 3.746 | -7.2497 | 1.7212 | -3.5303 | 7.5461 | -0.5403 | 0.2825 | -0.5866 | -0.3055 | 0.2212 | -0.2717 | 0.8436 | -0.2914 | 0.3191 | 0.0773 | -0.0658 | 0.0354 | 0.0142 | -0.093 | 0.0285 | 30.6375 | -8.6454 | 4.2754 | 8 | 1.9469 | 0.0803 | -0.2254 | 2.9302 | 0.5895 | 2.5215 | -0.0063 | 0.0302 | 0.0567 | -0.0394 | 0.0605 | -0.0301 | -0.0287 | -0.1923 | -0.0542 | 0.0472 | 0.001 | -0.0047 | 0.0381 | 0.0153 | 0.0414 | 29.0377 | 2.6315 | 18.8657 | 9 | 9.2118 | -0.1451 | -3.8616 | 10.5689 | 8.077 | 11.3515 | -0.1368 | 0.1741 | -0.889 | 0.5707 | 0.2847 | -0.4421 | 1.2399 | 0.5839 | -0.1479 | 0.0776 | 0.0778 | -0.0305 | 0.0108 | -0.0775 | 0.0676 | 19.0932 | -11.2401 | 31.9007 | 10 | 6.0909 | 0.7311 | 1.7081 | 1.7117 | 0.1042 | 5.3292 | -0.1758 | 0.4025 | -0.0544 | -0.0224 | 0.2757 | 0.0226 | -0.0745 | 0.103 | -0.0999 | 0.0146 | -0.0302 | 0.0166 | 0.0628 | -0.0015 | 0.0162 | 14.2706 | -2.5286 | 29.5727 | 11 | 5.637 | 6.298 | -0.6855 | 14.4224 | -0.3584 | 0.1058 | -0.8955 | 1.6635 | 2.5075 | -1.9048 | 0.0276 | -0.1427 | -0.6074 | 0.7948 | 0.8678 | 0.2336 | -0.0537 | -0.0662 | 0.1067 | 0.1436 | 0.0035 | 11.3583 | 10.4669 | 22.6442 | 12 | 3.7882 | -3.7634 | 0.6187 | 16.9594 | 2.1642 | 0.6852 | -0.3624 | 0.9614 | 0.2425 | -1.0734 | 0.1982 | -0.121 | -0.3508 | 0.2992 | 0.1642 | 0.1167 | -0.1497 | -0.0549 | 0.1956 | 0.087 | -0.1067 | 8.2185 | 1.9464 | 18.3808 | 13 | 14.8036 | 7.0092 | 7.7555 | 13.3612 | 6.1341 | 4.6666 | 0.0365 | 0.3612 | -1.1003 | -0.5279 | -0.0024 | -0.1615 | 0.115 | 0.1798 | -0.0342 | 0.0209 | -0.071 | 0.0458 | 0.1206 | -0.0686 | -0.0062 | 9.4905 | -8.0511 | 20.3843 | 14 | 1.6296 | 0.4162 | 1.0477 | 1.097 | 1.2379 | 1.6241 | -0.1326 | 0.1737 | 0.0808 | -0.1762 | 0.0772 | 0.0345 | -0.1339 | 0.0543 | 0.0554 | 0.0409 | -0.0244 | -0.0043 | 0.0177 | 0.0067 | 0.059 | 12.4687 | 2.5168 | 33.2096 | 15 | 6.6522 | 5.7209 | 0.8999 | 9.2285 | 1.7999 | 0.3661 | -0.1678 | -0.2329 | -0.1945 | 0.0449 | 0.0362 | 0.2118 | 0.0966 | -0.0934 | 0.1316 | 0.0332 | -0.0028 | 0.0216 | 0.038 | 0.0282 | 0.0753 | 6.8807 | -3.1217 | 46.7845 | 16 | 0.6835 | 0.5556 | -0.0146 | 0.972 | 0.6337 | 0.8802 | -0.1178 | 0.0074 | 0.0992 | -0.1399 | 0.0105 | 0.1507 | -0.0914 | -0.068 | 0.1073 | 0.042 | -0.0025 | -0.0327 | 0.0038 | 0.0067 | 0.0721 | 9.2015 | 5.6985 | 39.5634 | 17 | 1.7822 | -0.3776 | 2.3721 | 3.7954 | 3.0433 | 6.5411 | -0.0641 | 0.5246 | -0.2679 | -0.4224 | -0.1344 | 0.2675 | -0.2267 | 0.0352 | 0.1985 | 0.0267 | -0.03 | -0.0178 | 0.0701 | -0.0592 | 0.0039 | -1.3399 | -4.8203 | 17.6775 | 18 | 0.4318 | 0.825 | 1.2012 | 1.7849 | 1.9927 | 5.1649 | -0.2926 | 0.0837 | 0.2386 | -0.3652 | -0.0091 | 0.3159 | -0.552 | -0.2046 | 0.3017 | 0.0659 | -0.0085 | -0.096 | -0.0106 | 0.0237 | 0.0605 | 3.6034 | 7.24 | 29.3106 | 19 | 5.4393 | -1.487 | 1.116 | 2.2246 | -0.514 | 2.6347 | -0.0421 | 0.0516 | -0.1236 | -0.0665 | 0.0119 | 0.1164 | 0.0773 | 0.0111 | 0.0302 | 0.057 | -0.0166 | 0.0066 | 0.0121 | -0.0013 | 0.0646 | 12.7731 | -2.9149 | 40.2902 |
|
---|
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 - 57 | 24 - 57 | 5 | X-RAY DIFFRACTION | 5 | AA58 - 77 | 58 - 77 | 6 | X-RAY DIFFRACTION | 6 | AA78 - 96 | 78 - 96 | 7 | X-RAY DIFFRACTION | 7 | AA97 - 104 | 97 - 104 | 8 | X-RAY DIFFRACTION | 8 | AA105 - 124 | 105 - 124 | 9 | X-RAY DIFFRACTION | 9 | BB1 - 6 | 1 - 6 | 10 | X-RAY DIFFRACTION | 10 | BB7 - 14 | 7 - 14 | 11 | X-RAY DIFFRACTION | 11 | BB15 - 23 | 15 - 23 | 12 | X-RAY DIFFRACTION | 12 | BB24 - 31 | 24 - 31 | 13 | X-RAY DIFFRACTION | 13 | BB32 - 39 | 32 - 39 | 14 | X-RAY DIFFRACTION | 14 | BB40 - 59 | 40 - 59 | 15 | X-RAY DIFFRACTION | 15 | BB60 - 70 | 60 - 70 | 16 | X-RAY DIFFRACTION | 16 | BB71 - 83 | 71 - 83 | 17 | X-RAY DIFFRACTION | 17 | BB84 - 96 | 84 - 96 | 18 | X-RAY DIFFRACTION | 18 | BB97 - 106 | 97 - 106 | 19 | X-RAY DIFFRACTION | 19 | BB107 - 124 | 107 - 124 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|