ソフトウェア | 名称 | バージョン | 分類 |
---|
BOS | | データ収集 | PHASER | | 位相決定 | REFMAC | 5.5.0109精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | |
|
---|
精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW 解像度: 2.15→46.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.683 / SU ML: 0.126 / Isotropic thermal model: ISOTROPIC, TLS / 交差検証法: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.189 / 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 | 0.2322 | 2354 | 5 % | RANDOM |
---|
Rwork | 0.18656 | - | - | - |
---|
obs | 0.18883 | 44279 | 99.97 % | - |
---|
all | - | 46727 | - | - |
---|
|
---|
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: 31.523 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 0.47 Å2 | -0 Å2 | 0 Å2 |
---|
2- | - | -2.03 Å2 | -0 Å2 |
---|
3- | - | - | 1.55 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 2.15→46.37 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 5700 | 0 | 28 | 301 | 6029 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.014 | 0.022 | 5917 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 3909 | X-RAY DIFFRACTION | r_angle_refined_deg1.345 | 1.96 | 8021 | X-RAY DIFFRACTION | r_angle_other_deg0.906 | 3 | 9541 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.192 | 5 | 737 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.035 | 24.25 | 280 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.267 | 15 | 1004 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg22.633 | 15 | 31 | X-RAY DIFFRACTION | r_chiral_restr0.076 | 0.2 | 924 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 6554 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1225 | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.71 | 1.5 | 3620 | X-RAY DIFFRACTION | r_mcbond_other0.208 | 1.5 | 1497 | X-RAY DIFFRACTION | r_mcangle_it1.295 | 2 | 5859 | X-RAY DIFFRACTION | r_scbond_it2.112 | 3 | 2297 | X-RAY DIFFRACTION | r_scangle_it3.36 | 4.5 | 2151 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|
Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION Dom-ID | Auth asym-ID | 数 | タイプ | Rms dev position (Å) | Weight position |
---|
1 | A1420 | medium positional0.37 | 0.5 | 2 | B1420 | medium positional0.35 | 0.5 | 3 | C1420 | medium positional0.41 | 0.5 | 4 | D1420 | medium positional0.38 | 0.5 | 1 | A658 | loose positional0.34 | 5 | 2 | B658 | loose positional0.41 | 5 | 3 | C658 | loose positional0.77 | 5 | 4 | D658 | loose positional0.42 | 5 | 1 | A1420 | medium thermal0.76 | 2 | 2 | B1420 | medium thermal0.76 | 2 | 3 | C1420 | medium thermal0.87 | 2 | 4 | D1420 | medium thermal0.88 | 2 | 1 | A658 | loose thermal0.76 | 10 | 2 | B658 | loose thermal0.75 | 10 | 3 | C658 | loose thermal0.78 | 10 | 4 | D658 | loose thermal0.83 | 10 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|
LS精密化 シェル | 解像度: 2.15→2.206 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.268 | 175 | - |
---|
Rwork | 0.205 | 3227 | - |
---|
obs | - | - | 99.88 % |
---|
|
---|
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 | 0.742 | 0.6103 | -0.1595 | 3.1705 | -0.8562 | 0.7372 | -0.1223 | 0.0726 | -0.0281 | -0.5656 | 0.1186 | -0.2367 | -0.1035 | -0.0197 | 0.0038 | 0.2309 | -0.0299 | 0.0722 | 0.0654 | -0.0344 | 0.0834 | 38.311 | 9.4955 | 105.5522 | 2 | 0.8212 | 0.0927 | -0.0097 | 2.9523 | 0.4802 | 0.9947 | -0.0625 | 0.0223 | -0.0736 | 0.1067 | 0.0234 | 0.0407 | 0.1359 | -0.0981 | 0.0391 | 0.0266 | -0.0159 | 0.0244 | 0.0525 | -0.0404 | 0.0893 | 26.9225 | -21.4252 | 119.5174 | 3 | 1.001 | 0.5532 | -0.0143 | 3.424 | -0.9541 | 2.5655 | 0.0924 | -0.1571 | -0.2398 | 0.4891 | -0.1441 | -0.3416 | 0.4534 | 0.2384 | 0.0517 | 0.2428 | 0.0318 | -0.0928 | 0.1117 | 0.0233 | 0.1438 | 37.5456 | -1.9476 | 146.5811 | 4 | 0.9801 | -0.1916 | -0.1568 | 2.0897 | 0.3265 | 1.0217 | 0.0256 | 0.0891 | 0.0602 | -0.0306 | -0.0436 | 0.0683 | -0.101 | -0.0898 | 0.0181 | 0.0138 | 0.0042 | -0.012 | 0.086 | -0.0248 | 0.0707 | 26.8646 | 28.9106 | 133.5254 |
|
---|
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 | A-10 - 9999 | 2 | X-RAY DIFFRACTION | 2 | B-10 - 9999 | 3 | X-RAY DIFFRACTION | 3 | C-10 - 9999 | 4 | X-RAY DIFFRACTION | 4 | D-10 - 9999 | | | | |
|
---|