ソフトウェア | 名称: REFMAC / バージョン: 5.2.0019 / 分類: 精密化 |
---|
精密化 | 構造決定の手法: 分子置換 / 解像度: 1.8→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.418 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.126 / 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 | 0.21597 | 2915 | 5 % | RANDOM |
---|
Rwork | 0.18755 | - | - | - |
---|
obs | 0.18898 | 55608 | 96.44 % | - |
---|
|
---|
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: BABINET MODEL WITH MASK |
---|
原子変位パラメータ | Biso mean: 21.443 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 1.09 Å2 | 0 Å2 | -0.31 Å2 |
---|
2- | - | -0.66 Å2 | 0 Å2 |
---|
3- | - | - | -0.57 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 1.8→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 5006 | 0 | 62 | 453 | 5521 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.009 | 0.022 | 5214 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 3634 | X-RAY DIFFRACTION | r_angle_refined_deg1.194 | 1.968 | 7054 | X-RAY DIFFRACTION | r_angle_other_deg0.86 | 3 | 8826 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.624 | 5 | 608 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.266 | 24.08 | 250 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.039 | 15 | 906 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.747 | 15 | 28 | X-RAY DIFFRACTION | r_chiral_restr0.074 | 0.2 | 728 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 5726 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1086 | X-RAY DIFFRACTION | r_nbd_refined0.209 | 0.2 | 1116 | X-RAY DIFFRACTION | r_nbd_other0.193 | 0.2 | 3817 | X-RAY DIFFRACTION | r_nbtor_refined0.184 | 0.2 | 2554 | X-RAY DIFFRACTION | r_nbtor_other0.083 | 0.2 | 2460 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.135 | 0.2 | 397 | 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_refined0.136 | 0.2 | 17 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.124 | 0.2 | 42 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.148 | 0.2 | 25 | 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_it0.642 | 1.5 | 3975 | X-RAY DIFFRACTION | r_mcbond_other0.12 | 1.5 | 1220 | X-RAY DIFFRACTION | r_mcangle_it0.708 | 2 | 4958 | X-RAY DIFFRACTION | r_scbond_it1.331 | 3 | 2621 | X-RAY DIFFRACTION | r_scangle_it1.928 | 4.5 | 2096 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / 数: 4303 / Refine-ID: X-RAY DIFFRACTION タイプ | Rms dev position (Å) | Weight position |
---|
medium positional0.12 | 0.5 | medium thermal0.3 | 2 | | |
|
---|
LS精密化 シェル | 解像度: 1.8→1.847 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
---|
Rfree | 0.299 | 183 | - |
---|
Rwork | 0.265 | 3976 | - |
---|
obs | - | - | 92.22 % |
---|
|
---|
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 | 0.6188 | 0.0544 | -0.008 | 1.6413 | 0.5003 | 1.9107 | 0.0415 | -0.0403 | 0.0376 | 0.0015 | -0.0108 | 0.0445 | -0.0537 | -0.0254 | -0.0307 | -0.1318 | -0.0057 | 0.0049 | -0.114 | -0.0003 | -0.1189 | -1.1074 | -10.0625 | 38.7146 | 2 | 0.8763 | -0.2278 | -0.2786 | 1.5129 | 0.08 | 1.5562 | 0.0027 | 0.0634 | -0.0285 | -0.0759 | 0.0067 | 0.0347 | 0.0373 | -0.0085 | -0.0094 | -0.1347 | 0.0109 | -0.0141 | -0.1238 | -0.0062 | -0.1335 | 6.0839 | -39.9402 | 8.813 |
|
---|
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 | AA3 - 309 | 3 - 309 | 2 | X-RAY DIFFRACTION | 1 | AC501 | 1 | 3 | X-RAY DIFFRACTION | 2 | BB10 - 310 | 10 - 310 | 4 | X-RAY DIFFRACTION | 2 | BD502 | 1 | | | | | | | | |
|
---|