ソフトウェア 名称 バージョン 分類 HKL-2000データ収集 SOLVE位相決定 REFMAC5.2.0019精密化 HKL-2000データ削減 HKL-2000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 3EK6解像度 : 2.56→27.3 Å / Cor.coef. Fo :Fc : 0.948 / Cor.coef. Fo :Fc free : 0.919 / SU B : 21.137 / SU ML : 0.231 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / ESU R : 0.709 / ESU R Free : 0.305 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was ... 詳細 : Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was changed to N of the next residueRfactor 反射数 %反射 Selection details Rfree 0.25157 2814 5.1 % RANDOM Rwork 0.20626 - - - obs 0.20858 52509 98.95 % -
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 : 55.136 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.46 Å2 0 Å2 0 Å2 2- - 1.2 Å2 0 Å2 3- - - -2.66 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.56→27.3 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 10785 0 192 507 11484
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_d0.012 0.022 11115 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.382 2.001 15012 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg4.843 5 1429 X-RAY DIFFRACTION r_dihedral_angle_2_deg40.421 23.304 457 X-RAY DIFFRACTION r_dihedral_angle_3_deg17.823 15 1958 X-RAY DIFFRACTION r_dihedral_angle_4_deg18.391 15 102 X-RAY DIFFRACTION r_chiral_restr0.083 0.2 1723 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.02 8168 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refined0.268 0.3 5582 X-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refined0.33 0.5 7651 X-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refined0.219 0.5 802 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.361 0.3 48 X-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refined0.265 0.5 12 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_it1.041 2 7197 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it1.755 3 11179 X-RAY DIFFRACTION r_scbond_it1.025 2 4324 X-RAY DIFFRACTION r_scangle_it1.766 3 3833 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
Refine LS restraints NCS Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (7 x 18) 大きな表を隠す Ens-ID Dom-ID Auth asym-ID 数 タイプ Rms dev position (Å)Weight position 1 1 A1789 medium positional0.62 0.5 1 2 C1789 medium positional0.68 0.5 1 3 D1789 medium positional0.62 0.5 2 1 B1789 medium positional0.74 0.5 2 2 E1789 medium positional0.68 0.5 2 3 F1789 medium positional0.69 0.5 3 1 A1789 medium positional0.64 0.5 4 1 C1796 medium positional0.58 0.5 5 1 E1789 medium positional0.58 0.5 1 1 A1789 medium thermal0.99 2 1 2 C1789 medium thermal1.16 2 1 3 D1789 medium thermal1.12 2 2 1 B1789 medium thermal2.59 2 2 2 E1789 medium thermal1.03 2 2 3 F1789 medium thermal1.73 2 3 1 A1789 medium thermal2.9 2 4 1 C1796 medium thermal1.04 2 5 1 E1789 medium thermal0.59 2
LS精密化 シェル 解像度 : 2.56→2.606 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.376 184 - Rwork 0.324 3531 - obs - - 91.34 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 6) 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 0.5456 -0.2217 -0.105 0.897 -0.0825 0.6997 0.0353 -0.0073 -0.0141 0.0651 -0.0197 0.0733 -0.045 0.005 -0.0156 -0.1155 -0.0112 0.0055 -0.0508 0.0218 -0.0067 -24.4705 13.7472 14.8793 2 0.3475 -0.5653 0.1755 1.2977 -0.4128 0.8379 -0.0674 -0.0767 0.0669 -0.0956 0.0302 -0.0302 0.1819 0.1251 0.0373 -0.0976 0.0589 0.0315 -0.0051 0.0403 -0.0396 3.4012 -12.4106 17.7926 3 0.3125 0.3667 -0.0724 0.4597 -0.3149 1.8136 0.0348 -0.038 0.0491 0.007 -0.0345 0.0697 -0.1423 0.1539 -0.0003 -0.1212 -0.0656 -0.0093 -0.0352 0.0002 0.0042 1.4834 30.3577 2.7161 4 0.4205 0.2756 0.1336 0.6175 0.3144 1.3616 -0.1522 0.1168 0.1045 -0.2058 0.0963 0.0271 0.0961 -0.125 0.0559 0.0601 -0.1596 -0.064 -0.0435 0.0401 -0.0737 -14.022 15.7806 -29.0058 5 0.6816 0.3914 -0.2102 0.6857 -0.2081 1.7039 -0.0471 -0.0865 0.0433 -0.2471 0.1221 0.0267 0.5061 -0.042 -0.075 0.1606 -0.0458 -0.0347 -0.1454 0.0145 -0.0798 -14.3074 -23.9887 -7.5938 6 1.1427 0.473 -0.0077 0.7808 -0.7739 1.1071 -0.1368 0.1642 -0.0257 -0.3378 -0.0092 -0.1019 0.3975 0.3155 0.1461 0.1475 0.0491 0.1493 -0.0014 0.024 -0.0753 12.3284 -3.4219 -25.7044
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-1 - 239 2 X-RAY DIFFRACTION 2 B2 - 240 3 X-RAY DIFFRACTION 3 C2 - 240 4 X-RAY DIFFRACTION 4 D2 - 240 5 X-RAY DIFFRACTION 5 E2 - 240 6 X-RAY DIFFRACTION 6 F2 - 239