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 : 2.4→20 Å / Cor.coef. Fo :Fc : 0.958 / Cor.coef. Fo :Fc free : 0.938 / SU B : 17.787 / SU ML : 0.216 / TLS residual ADP flag : LIKELY RESIDUAL / Isotropic thermal model : RESTRAINED / 交差検証法 : THROUGHOUT / ESU R : 0.383 / ESU R Free : 0.254 / 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 2R8V, 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 2R8V, 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 0.24394 1010 5.1 % RANDOM Rwork 0.19437 - - - obs 0.19694 18665 99.52 % - all - 19707 - -
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 : 45.527 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.25 Å2 0.63 Å2 0 Å2 2- - 1.25 Å2 0 Å2 3- - - -1.88 Å2
Refine analyze Free Obs Luzzati coordinate error 0.55 Å 0.38 Å Luzzati d res low - 5 Å Luzzati sigma a 0.49 Å 0.4 Å
精密化ステップ サイクル : LAST / 解像度 : 2.4→20 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3227 0 51 92 3370
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_d0.01 0.021 3333 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg2.07 1.974 4514 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg9.703 5 422 X-RAY DIFFRACTION r_dihedral_angle_2_deg39.022 22.763 152 X-RAY DIFFRACTION r_dihedral_angle_3_deg23.46 15 541 X-RAY DIFFRACTION r_dihedral_angle_4_deg21.411 15 34 X-RAY DIFFRACTION r_chiral_restr0.198 0.2 511 X-RAY DIFFRACTION r_gen_planes_refined0.022 0.02 2530 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refined0.293 0.3 1534 X-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refined0.331 0.5 2204 X-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refined0.193 0.5 169 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.278 0.3 76 X-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refined0.213 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_it2.531 1.5 2137 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it3.674 2 3316 X-RAY DIFFRACTION r_scbond_it6.423 3 1315 X-RAY DIFFRACTION r_scangle_it8.942 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 : 2.4→2.463 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.328 73 - Rwork 0.271 1360 - obs - - 97.68 %
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 1.8106 0.4082 -0.0945 2.8542 -0.4495 0.8188 0.0529 0.0766 0.0112 0.1434 0.0118 0.4471 0.0462 -0.0778 -0.0647 0.1235 -0.0141 -0.0642 0.1334 0.0473 0.1308 19.0408 24.2537 39.4259 2 1.2235 3.3571 3.2579 9.2115 8.939 8.6747 -0.5499 -1.5382 1.0344 -2.2499 0.0562 1.0586 -1.502 2.0652 0.4937 0.5566 -0.097 -0.2893 0.5413 0.4429 0.6513 5.6267 48.3745 28.9203 3 2.5527 -0.7335 -0.5335 5.8361 -4.2739 6.5064 -0.0171 -0.1364 0.4919 0.0243 0.0425 0.4149 0.2054 -0.0791 -0.0254 -0.0009 0.007 -0.0321 0.0718 0.008 0.2535 16.677 42.2245 42.127 4 1.5597 0.003 0.4373 2.0961 -0.2655 0.9269 -0.0163 0.3076 0.2496 -0.3119 -0.031 0.243 -0.0783 0.0487 0.0474 0.1381 0.011 -0.0647 0.1007 0.0768 0.1113 23.2906 38.6671 29.951 5 10.9041 2.6542 2.0629 0.7268 0.6409 4.6364 0.2235 0.4882 -0.0382 -0.1659 -0.2206 0.0616 0.0291 0.0824 -0.0029 0.1246 0.0892 -0.0722 0.1563 -0.0114 -0.028 16.0757 26.5569 19.0574 6 1.4975 -1.8549 -0.9879 2.3583 0.7808 3.8882 -0.1455 0.2688 -0.3886 0.0579 0.0743 0.4122 0.5414 -0.3272 0.0712 0.1165 -0.0067 -0.097 0.1565 0.0136 0.1333 15.1764 19.2514 32.2353 7 4.7342 -1.3531 1.2418 6.687 -1.5595 6.6237 -0.4127 0.2474 0.2058 -0.9133 0.3701 -0.7704 -0.4133 0.329 0.0426 0.2487 -0.3244 0.1898 0.0482 -0.1419 0.0526 38.9948 4.5159 2.8526 8 5.0326 6.5515 1.3461 11.9304 -1.0024 2.5909 -0.6068 0.3947 -0.2339 -1.0588 0.661 -0.9863 -0.3171 0.5125 -0.0542 0.3055 -0.2507 0.1702 0.1286 -0.1211 0.0093 34.1244 2.7544 0.0273 9 2.6014 1.1985 1.648 3.563 0.4599 2.8059 -0.1009 -0.2139 0.1568 -0.1764 0.1578 0.0196 -0.4067 -0.0958 -0.0569 0.1541 -0.0866 0.1146 0.1207 -0.109 0.0296 29.9406 0.735 10.8527 10 2.6601 -0.2045 0.3448 7.5792 3.2468 5.85 0.0245 -0.2733 -0.1262 -0.084 0.295 -0.1452 0.1357 -0.3671 -0.3196 0.1356 -0.1533 0.0529 0.2331 -0.0544 0.0167 30.2583 -10.308 14.0813
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 - 68 25 - 88 2 X-RAY DIFFRACTION 2 AA69 - 84 89 - 104 3 X-RAY DIFFRACTION 3 AA85 - 125 105 - 145 4 X-RAY DIFFRACTION 4 AA126 - 217 146 - 237 5 X-RAY DIFFRACTION 5 AA218 - 256 238 - 276 6 X-RAY DIFFRACTION 6 AA257 - 283 277 - 303 7 X-RAY DIFFRACTION 7 AA284 - 316 304 - 336 8 X-RAY DIFFRACTION 8 AA317 - 347 337 - 367 9 X-RAY DIFFRACTION 9 AA348 - 396 368 - 416 10 X-RAY DIFFRACTION 10 AA397 - 436 417 - 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