ソフトウェア 名称 バージョン 分類 REFMAC5.2.0005精密化 CrystalClearデータ収集 HKL-2000データ削減 HKL-2000データスケーリング SHELXS位相決定 CNS1.1 精密化
精密化 構造決定の手法 : 多波長異常分散 / 解像度 : 2.5→20 Å / Cor.coef. Fo :Fc : 0.959 / Cor.coef. Fo :Fc free : 0.922 / SU B : 17.872 / SU ML : 0.222 / TLS residual ADP flag : LIKELY RESIDUAL / Isotropic thermal model : RESTRAINED / 交差検証法 : THROUGHOUT / ESU R : 0.537 / ESU R Free : 0.293 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. For this and related entry 2R98, The structures were solved by MAD datasets collect at three wavelengths at Se edge. After the first ... 詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. For this and related entry 2R98, The structures were solved by MAD datasets collect at three wavelengths at Se edge. After the first structural model was built, the refinements were carried on against different datasets since they are in same space group and a similar unit cell.Rfactor 反射数 %反射 Selection details Rfree 0.25234 872 5 % RANDOM Rwork 0.19153 - - - obs 0.19438 16396 98.94 % -
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原子変位パラメータ Biso mean : 27.591 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.76 Å2 0.88 Å2 0 Å2 2- - 1.76 Å2 0 Å2 3- - - -2.64 Å2
Refine analyze Free Obs Luzzati coordinate error 0.53 Å 0.37 Å Luzzati d res low - 5 Å Luzzati sigma a 0.48 Å 0.39 Å
精密化ステップ サイクル : LAST / 解像度 : 2.5→20 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3227 0 51 117 3395
拘束条件 大きな表を表示 (5 x 33) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.011 0.021 3333 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg2.041 1.974 4514 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg7.672 5 422 X-RAY DIFFRACTION r_dihedral_angle_2_deg40.201 22.763 152 X-RAY DIFFRACTION r_dihedral_angle_3_deg20.874 15 541 X-RAY DIFFRACTION r_dihedral_angle_4_deg19.592 15 34 X-RAY DIFFRACTION r_chiral_restr0.146 0.2 511 X-RAY DIFFRACTION r_gen_planes_refined0.02 0.02 2530 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refined0.304 0.3 1634 X-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refined0.337 0.5 2294 X-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refined0.217 0.5 202 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.334 0.3 81 X-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refined0.317 0.5 15 X-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it2.893 1.5 2141 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it3.709 2 3316 X-RAY DIFFRACTION r_scbond_it6.513 3 1313 X-RAY DIFFRACTION r_scangle_it8.66 4.5 1198 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
LS精密化 シェル 解像度 : 2.5→2.567 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.294 73 - Rwork 0.282 1185 - obs - - 98.13 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 10) 大きな表を隠す 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 1.609 -0.4794 -0.1819 4.7133 -0.9343 0.6852 0.1865 0.0384 -0.129 0.0039 -0.1663 0.4775 0.0584 -0.0508 -0.0202 0.2131 -0.062 -0.0898 0.1525 0.0575 0.1753 18.6477 24.4709 39.5797 2 24.5131 8.24 -10.6561 9.1113 10.8413 42.0799 0.691 0.1663 3.1976 -0.1985 0.8712 0.7528 0.985 -1.9203 -1.5622 -0.1596 0.1773 -0.0949 -0.4761 0.4708 0.5938 5.6202 48.7367 28.3505 3 1.5807 0.8769 -0.7401 0.5179 -0.0805 3.8113 0.1438 0.0277 0.3444 -0.067 -0.2581 0.4144 0.0872 -0.0004 0.1143 0.1315 0.0313 -0.006 0.0528 0.0749 0.2754 14.9987 45.3414 40.0873 4 1.8709 -0.0293 0.8522 1.7114 -0.5248 1.3829 0.1205 0.0997 0.2094 -0.0602 -0.1124 0.0865 -0.0961 0.0987 -0.0081 0.2168 0.013 -0.0001 0.1409 0.0714 0.1286 25.0663 39.6185 32.6298 5 9.1742 -1.5704 0.0808 8.0736 -2.8201 6.6738 0.4005 0.3823 -0.4683 -0.5008 -0.3166 0.6547 0.0069 -0.4456 -0.0839 0.0192 0.0635 -0.1798 0.1202 -0.0705 0.0575 10.1795 24.6461 18.9414 6 4.2612 -0.2996 -2.2572 2.5179 0.2923 5.4936 -0.0363 0.0645 -0.5625 -0.1599 -0.2995 0.1799 0.1783 0.0909 0.3359 0.2428 0.086 -0.1214 0.1586 0.0012 0.216 19.0446 25.7368 26.4188 7 3.5963 -1.8621 -3.3626 6.541 -3.1214 11.2758 0.1752 0.0595 -0.7557 0.1049 -0.0206 0.5521 0.4779 -0.6637 -0.1546 0.131 -0.0357 -0.1712 0.0242 0.0128 0.1475 16.6931 17.1274 31.418 8 5.6107 -1.8799 2.2911 6.8141 -2.1144 5.1236 -0.3081 0.4478 0.391 -0.0521 0.1066 -0.3468 -0.9545 0.4389 0.2015 0.2467 -0.1483 0.0799 0.021 -0.0789 0.1317 38.7201 5.9638 3.0783 9 22.5225 -4.1792 6.7148 12.3199 -14.4607 17.1288 -0.5392 -0.9911 -1.3103 -1.6803 0.6417 -0.6733 0.3291 1.511 -0.1025 0.1419 -0.3026 0.2623 0.0096 -0.4802 -0.0623 37.3237 -3.6272 -3.5869 10 2.3393 0.9084 1.3572 5.2212 0.0877 3.5562 -0.0217 -0.2666 0.1445 0.1064 0.0461 -0.0391 -0.0918 -0.3267 -0.0244 0.1601 -0.0566 0.0586 0.2084 -0.1166 0.107 30.4703 -2.7203 10.9783
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 AA5 - 69 25 - 89 2 X-RAY DIFFRACTION 2 AA70 - 84 90 - 104 3 X-RAY DIFFRACTION 3 AA85 - 109 105 - 129 4 X-RAY DIFFRACTION 4 AA110 - 207 130 - 227 5 X-RAY DIFFRACTION 5 AA208 - 241 228 - 261 6 X-RAY DIFFRACTION 6 AA242 - 265 262 - 285 7 X-RAY DIFFRACTION 7 AA266 - 283 286 - 303 8 X-RAY DIFFRACTION 8 AA284 - 313 304 - 333 9 X-RAY DIFFRACTION 9 AA314 - 327 334 - 347 10 X-RAY DIFFRACTION 10 AA328 - 436 348 - 456
Xplor file Refine-ID Serial no Param file Topol file X-RAY DIFFRACTION 1 protein_rep.paramprotein.topX-RAY DIFFRACTION 2 water_rep.paramwater.topX-RAY DIFFRACTION 3 ion.paramion.topX-RAY DIFFRACTION 4 ligand.paramligand.topX-RAY DIFFRACTION 5 ACO.paramACO.top