ソフトウェア 名称 バージョン 分類 ADSCQuantumデータ収集 PHASER位相決定 REFMAC5.5.0102精密化 MOSFLMデータ削減 SCALA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 3F6N解像度 : 2.59→18.98 Å / Cor.coef. Fo :Fc : 0.947 / Cor.coef. Fo :Fc free : 0.911 / SU B : 33.25 / SU ML : 0.311 / TLS residual ADP flag : LIKELY RESIDUAL / Isotropic thermal model : TLS REFINEMENT 4 GROUPS / 交差検証法 : THROUGHOUT / ESU R Free : 0.391 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : WEIGHT MATRIX 0.035Rfactor 反射数 %反射 Selection details Rfree 0.289 657 7.1 % RANDOM Rwork 0.219 - - - obs 0.223 8660 96.1 % - all - 9317 - -
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 : 25.07 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.03 Å2 0 Å2 -0.08 Å2 2- - -0.07 Å2 0 Å2 3- - - 0.03 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.59→18.98 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2153 0 1 29 2183
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 0.022 2171 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.255 2.015 2927 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg5.391 5 280 X-RAY DIFFRACTION r_dihedral_angle_2_deg42.551 30 86 X-RAY DIFFRACTION r_dihedral_angle_3_deg20.609 15 468 X-RAY DIFFRACTION r_dihedral_angle_4_degX-RAY DIFFRACTION r_chiral_restr0.085 0.2 371 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.021 1500 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refinedX-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refinedX-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refinedX-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refinedX-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refinedX-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it0.373 1.5 1414 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it0.722 2 2294 X-RAY DIFFRACTION r_scbond_it1.274 3 757 X-RAY DIFFRACTION r_scangle_it2.187 4.5 633 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 : 2.59→2.65 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.44 51 - Rwork 0.307 618 - obs - - 99.11 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 4) 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 8.0085 3.7416 9.0064 2.9031 6.6741 15.4977 0.0963 0.3411 -0.2461 0.128 0.0537 -0.0297 0.4047 0.0757 -0.15 0.3462 -0.0759 0.1228 0.0963 0.0207 0.3788 44.707 14.896 33.418 2 5.9853 1.8632 9.4293 0.5922 2.9433 14.9008 0.0348 1.0522 -0.1775 0.083 0.2694 0.0273 0.1583 1.5074 -0.3042 0.9189 -0.1008 0.244 1.1426 -0.3757 0.9101 26.619 6.78 10.551 3 8.6028 1.7426 6.2067 4.1179 2.9202 12.6448 -0.0196 0.3547 -0.1758 0.0944 0.3656 -0.1087 -0.0347 1.1541 -0.346 0.3387 -0.1046 0.1086 0.707 -0.2382 0.449 13.741 2.558 -4.219 4 12.6134 3.9628 10.5499 10.973 3.5073 17.617 0.0902 0.1911 -0.0709 0.5813 0.5375 -0.7238 -0.1406 1.6196 -0.6277 0.3262 -0.0138 0.0775 0.6189 -0.308 0.5163 -1.897 -3.274 -21.221
精密化 TLSグループ 大きな表を表示 (5 x 16) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A2 - 32 2 X-RAY DIFFRACTION 1 B3 - 32 3 X-RAY DIFFRACTION 1 C2 - 32 4 X-RAY DIFFRACTION 1 D3 - 32 5 X-RAY DIFFRACTION 2 A33 - 40 6 X-RAY DIFFRACTION 2 B33 - 40 7 X-RAY DIFFRACTION 2 C33 - 40 8 X-RAY DIFFRACTION 2 D33 - 40 9 X-RAY DIFFRACTION 3 A41 - 59 10 X-RAY DIFFRACTION 3 B41 - 59 11 X-RAY DIFFRACTION 3 C41 - 59 12 X-RAY DIFFRACTION 3 D41 - 59 13 X-RAY DIFFRACTION 4 A60 - 71 14 X-RAY DIFFRACTION 4 B60 - 73 15 X-RAY DIFFRACTION 4 C60 - 74 16 X-RAY DIFFRACTION 4 D60 - 70