ソフトウェア | 名称 | バージョン | 分類 | NB |
---|
REFMAC | 5.2.0019精密化 | | PDB_EXTRACT | 3.005 | データ抽出 | | HKL-2000 | | データ収集 | | HKL-2000 | | データ削減 | | SCALEPACK | | データスケーリング | | SOLVE | | 位相決定 | | |
|
---|
精密化 | 構造決定の手法: 単一同系置換・異常分散 / 解像度: 2→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.359 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.174 / 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 | 0.259 | 1733 | 5 % | RANDOM |
---|
Rwork | 0.213 | - | - | - |
---|
obs | 0.215 | 34349 | 99.96 % | - |
---|
|
---|
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 max: 64.1 Å2 / Biso mean: 29.651 Å2 / Biso min: 13.15 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.35 Å2 | -0.18 Å2 | 0 Å2 |
---|
2- | - | -0.35 Å2 | 0 Å2 |
---|
3- | - | - | 0.53 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 3356 | 0 | 0 | 194 | 3550 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.02 | 0.022 | 3416 | X-RAY DIFFRACTION | r_angle_refined_deg2.064 | 1.989 | 4660 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg8.538 | 5 | 434 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.917 | 25 | 156 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.17 | 15 | 568 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.123 | 15 | 26 | X-RAY DIFFRACTION | r_chiral_restr0.142 | 0.2 | 544 | X-RAY DIFFRACTION | r_gen_planes_refined0.009 | 0.02 | 2626 | X-RAY DIFFRACTION | r_nbd_refined0.23 | 0.2 | 1539 | X-RAY DIFFRACTION | r_nbtor_refined0.316 | 0.2 | 2361 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.148 | 0.2 | 210 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.28 | 0.2 | 74 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.369 | 0.2 | 19 | X-RAY DIFFRACTION | r_mcbond_it1.21 | 1.5 | 2246 | X-RAY DIFFRACTION | r_mcangle_it1.852 | 2 | 3584 | X-RAY DIFFRACTION | r_scbond_it3.059 | 3 | 1292 | X-RAY DIFFRACTION | r_scangle_it4.819 | 4.5 | 1076 | | | | | | | | | | | | | | | | | |
|
---|
LS精密化 シェル | 解像度: 2.002→2.054 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.298 | 137 | - |
---|
Rwork | 0.213 | 2329 | - |
---|
all | - | 2466 | - |
---|
obs | - | - | 99.92 % |
---|
|
---|
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 | 5.1514 | 1.223 | -0.187 | 4.431 | -0.2425 | 2.7555 | 0.3113 | -0.7411 | -0.1018 | 0.3447 | -0.1657 | -0.0711 | 0.1459 | 0.0047 | -0.1455 | -0.0714 | -0.028 | -0.0795 | 0.0214 | -0.0083 | -0.1165 | 70.3343 | 20.7466 | 53.3825 | 2 | 4.5086 | 3.4158 | 0.4613 | 4.0413 | 0.1995 | 1.9872 | 0.1709 | -0.2397 | -0.0562 | 0.2738 | -0.2297 | -0.1646 | 0.061 | -0.0043 | 0.0587 | -0.138 | 0.0481 | -0.0392 | -0.1665 | 0.0009 | -0.1608 | 66.1472 | 15.0964 | 29.5125 | 3 | 2.4535 | 1.4843 | -0.4472 | 5.1738 | -0.5833 | 2.717 | 0.0365 | -0.2655 | -0.0435 | 0.1563 | 0.008 | -0.2108 | 0.0579 | 0.1819 | -0.0444 | -0.1009 | 0.0516 | -0.015 | -0.0429 | -0.0431 | -0.1268 | -36.3752 | 86.1043 | 90.236 | 4 | 3.5121 | 2.9371 | 0.4669 | 4.3959 | -0.1401 | 2.4732 | 0.1559 | -0.2358 | -0.0037 | 0.3164 | -0.22 | -0.0538 | 0.0702 | 0.1103 | 0.0641 | -0.1304 | 0.0451 | -0.0154 | -0.1389 | 0.0057 | -0.1675 | -39.7391 | 79.1999 | 66.5414 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | A0 - 98 | 2 | X-RAY DIFFRACTION | 2 | A103 - 217 | 3 | X-RAY DIFFRACTION | 3 | B0 - 98 | 4 | X-RAY DIFFRACTION | 4 | B103 - 217 | | | | |
|
---|