ソフトウェア | 名称 | バージョン | 分類 |
---|
REFMAC | 5.8.0258精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHENIX | | 位相決定 | |
|
---|
精密化 | 構造決定の手法: 分子置換 開始モデル: 6L4B 解像度: 3.4→47.824 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.831 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.222 / SU B: 69.859 / SU ML: 0.464 / Average fsc free: 0.9008 / Average fsc work: 0.9081 / 交差検証法: THROUGHOUT / ESU R Free: 0.568 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.2774 | 1332 | 5.013 % | RANDOM |
---|
Rwork | 0.2415 | 25238 | - | - |
---|
all | 0.243 | - | - | - |
---|
obs | - | 26570 | 96.992 % | - |
---|
|
---|
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: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT |
---|
原子変位パラメータ | Biso mean: 121.104 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -1.134 Å2 | -0.567 Å2 | -0 Å2 |
---|
2- | - | -1.134 Å2 | 0 Å2 |
---|
3- | - | - | 3.678 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 3.4→47.824 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 8670 | 0 | 0 | 0 | 8670 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.003 | 0.013 | 8855 | X-RAY DIFFRACTION | r_bond_other_d0.036 | 0.017 | 8083 | X-RAY DIFFRACTION | r_angle_refined_deg1.246 | 1.635 | 12041 | X-RAY DIFFRACTION | r_angle_other_deg2.296 | 1.567 | 18851 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.677 | 5 | 1110 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg31.621 | 24.368 | 451 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.709 | 15 | 1464 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg13.419 | 15 | 32 | X-RAY DIFFRACTION | r_chiral_restr0.046 | 0.2 | 1166 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 9942 | X-RAY DIFFRACTION | r_gen_planes_other0.004 | 0.02 | 1662 | X-RAY DIFFRACTION | r_nbd_refined0.225 | 0.2 | 2026 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.226 | 0.2 | 7904 | X-RAY DIFFRACTION | r_nbtor_refined0.154 | 0.2 | 4251 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.063 | 0.2 | 3608 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.168 | 0.2 | 123 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.175 | 0.2 | 6 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.248 | 0.2 | 21 | X-RAY DIFFRACTION | r_nbd_other0.221 | 0.2 | 40 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.284 | 0.2 | 3 | X-RAY DIFFRACTION | r_mcbond_it1.906 | 7.732 | 4461 | X-RAY DIFFRACTION | r_mcbond_other1.906 | 7.731 | 4460 | X-RAY DIFFRACTION | r_mcangle_it3.433 | 11.591 | 5564 | X-RAY DIFFRACTION | r_mcangle_other3.433 | 11.593 | 5565 | X-RAY DIFFRACTION | r_scbond_it1.627 | 7.837 | 4394 | X-RAY DIFFRACTION | r_scbond_other1.627 | 7.838 | 4395 | X-RAY DIFFRACTION | r_scangle_it2.866 | 11.69 | 6477 | X-RAY DIFFRACTION | r_scangle_other2.866 | 11.691 | 6478 | X-RAY DIFFRACTION | r_lrange_it4.888 | 90.967 | 9530 | X-RAY DIFFRACTION | r_lrange_other4.888 | 90.978 | 9531 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|
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 (%) |
---|
3.4-3.488 | 0.311 | 88 | 0.312 | 1701 | X-RAY DIFFRACTION | 91.229 | 3.488-3.583 | 0.314 | 86 | 0.308 | 1779 | X-RAY DIFFRACTION | 95.7392 | 3.583-3.686 | 0.299 | 97 | 0.289 | 1734 | X-RAY DIFFRACTION | 97.4454 | 3.686-3.799 | 0.317 | 77 | 0.278 | 1687 | X-RAY DIFFRACTION | 97.7827 | 3.799-3.923 | 0.317 | 98 | 0.259 | 1636 | X-RAY DIFFRACTION | 97.5253 | 3.923-4.06 | 0.271 | 88 | 0.249 | 1566 | X-RAY DIFFRACTION | 97.4087 | 4.06-4.212 | 0.315 | 89 | 0.246 | 1554 | X-RAY DIFFRACTION | 97.6233 | 4.212-4.383 | 0.282 | 78 | 0.21 | 1480 | X-RAY DIFFRACTION | 97.9258 | 4.383-4.576 | 0.238 | 80 | 0.196 | 1424 | X-RAY DIFFRACTION | 97.0949 | 4.576-4.797 | 0.203 | 88 | 0.199 | 1365 | X-RAY DIFFRACTION | 97.3208 | 4.797-5.054 | 0.233 | 67 | 0.197 | 1298 | X-RAY DIFFRACTION | 97.5697 | 5.054-5.357 | 0.241 | 60 | 0.209 | 1223 | X-RAY DIFFRACTION | 96.5387 | 5.357-5.723 | 0.255 | 58 | 0.213 | 1171 | X-RAY DIFFRACTION | 97.0008 | 5.723-6.174 | 0.313 | 59 | 0.224 | 1105 | X-RAY DIFFRACTION | 97.0809 | 6.174-6.753 | 0.267 | 48 | 0.244 | 1002 | X-RAY DIFFRACTION | 96.9529 | 6.753-7.533 | 0.27 | 45 | 0.238 | 953 | X-RAY DIFFRACTION | 98.6166 | 7.533-8.666 | 0.274 | 45 | 0.211 | 848 | X-RAY DIFFRACTION | 99.8881 | 8.666-10.535 | 0.245 | 32 | 0.206 | 739 | X-RAY DIFFRACTION | 99.8705 | 10.535-14.579 | 0.291 | 34 | 0.245 | 601 | X-RAY DIFFRACTION | 99.686 | 14.579-47.824 | 0.406 | 15 | 0.423 | 372 | X-RAY DIFFRACTION | 95.5556 |
|
---|
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 | 1.8726 | -1.0593 | -0.6615 | 1.5377 | 0.1831 | 0.4454 | 0.1664 | -0.0518 | 0.0809 | -0.19 | -0.0576 | -0.0895 | -0.0203 | 0.0286 | -0.1088 | 0.8222 | -0.0576 | 0.0541 | 0.3546 | 0.2774 | 0.4523 | 25.783 | -24.4557 | -53.1431 | 2 | 2.0372 | 0.9341 | 0.8847 | 1.6037 | 0.4922 | 0.9789 | 0.2054 | -0.0457 | 0.0615 | 0.0195 | -0.0914 | 0.093 | -0.0539 | -0.0052 | -0.114 | 0.7854 | -0.0059 | -0.0566 | 0.3693 | 0.2254 | 0.4897 | -10.4921 | -26.4076 | -48.5784 | 3 | 0.7975 | 0.0419 | 0.7451 | 1.1543 | -0.6119 | 1.6427 | 0.4252 | 0.0001 | -0.0421 | 0.1767 | -0.3367 | -0.1579 | 0.0924 | -0.052 | -0.0885 | 1.0885 | -0.4415 | -0.4244 | 0.5129 | 0.3806 | 0.3022 | 17.0444 | -39.9732 | -16.4747 | 4 | 0.5117 | 0.2709 | 0.2802 | 2.679 | -0.5572 | 0.9368 | 0.1141 | -0.0288 | 0.0342 | -0.0815 | 0.2319 | 0.057 | 0.2736 | -0.2356 | -0.346 | 1.0805 | -0.752 | -0.6307 | 0.5408 | 0.4621 | 0.4981 | -5.459 | -69.3376 | -12.7358 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | ALLA29 - 317 | 2 | X-RAY DIFFRACTION | 2 | ALLB29 - 317 | 3 | X-RAY DIFFRACTION | 3 | ALLC29 - 317 | 4 | X-RAY DIFFRACTION | 4 | ALLD29 - 317 | | | | | | | | |
|
---|