ソフトウェア 名称 バージョン 分類 REFMAC5.2.0019精密化 HKL-2000データ削減 HKL-2000データスケーリング SOLVE位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.4→20 Å / Cor.coef. Fo :Fc : 0.955 / Cor.coef. Fo :Fc free : 0.931 / SU B : 18.547 / SU ML : 0.191 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / σ(I) : 0 / ESU R : 0.384 / ESU R Free : 0.247 立体化学のターゲット値 : MAXIMUM LIKELIHOOD WITH PHASES詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.23347 5613 5 % RANDOM Rwork 0.18504 - - - all 0.18751 106381 - - obs 0.18751 106381 97.91 % -
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 : 33.891 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.53 Å2 0 Å2 2.45 Å2 2- - -1.97 Å2 0 Å2 3- - - 1.14 Å2
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 18993 0 153 541 19687
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 0.019 19626 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 13538 X-RAY DIFFRACTION r_angle_refined_deg1.404 1.891 26524 X-RAY DIFFRACTION r_angle_other_deg0.864 2.179 32811 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.955 5 2337 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.697 23.91 936 X-RAY DIFFRACTION r_dihedral_angle_3_deg17.784 15 3321 X-RAY DIFFRACTION r_dihedral_angle_4_deg20.204 15 108 X-RAY DIFFRACTION r_chiral_restr0.069 0.2 2760 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 21675 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 4203 X-RAY DIFFRACTION r_nbd_refined0.205 0.2 3601 X-RAY DIFFRACTION r_nbd_other0.199 0.2 13204 X-RAY DIFFRACTION r_nbtor_refined0.199 0.2 9335 X-RAY DIFFRACTION r_nbtor_other0.087 0.2 9242 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.143 0.2 540 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.261 0.2 14 X-RAY DIFFRACTION r_symmetry_vdw_other0.262 0.2 23 X-RAY DIFFRACTION r_symmetry_hbond_refined0.197 0.2 6 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_it1.058 1.5 14720 X-RAY DIFFRACTION r_mcbond_other0.153 1.5 4782 X-RAY DIFFRACTION r_mcangle_it1.079 2 18721 X-RAY DIFFRACTION r_scbond_it1.933 3 9317 X-RAY DIFFRACTION r_scangle_it2.79 4.5 7803 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
Refine LS restraints NCS Ens-ID : 1 / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (6 x 24) 大きな表を隠す Dom-ID Auth asym-ID 数 タイプ Rms dev position (Å)Weight position 1 A2277 medium positional0.27 0.5 2 B2277 medium positional0.26 0.5 3 C2277 medium positional0.38 0.5 4 D2277 medium positional0.23 0.5 5 E2277 medium positional0.19 0.5 6 F2277 medium positional0.35 0.5 1 A3057 loose positional0.59 5 2 B3057 loose positional0.69 5 3 C3057 loose positional0.63 5 4 D3057 loose positional0.6 5 5 E3057 loose positional0.55 5 6 F3057 loose positional0.71 5 1 A2277 medium thermal0.46 2 2 B2277 medium thermal0.51 2 3 C2277 medium thermal0.53 2 4 D2277 medium thermal0.48 2 5 E2277 medium thermal0.54 2 6 F2277 medium thermal0.44 2 1 A3057 loose thermal1.08 10 2 B3057 loose thermal1.13 10 3 C3057 loose thermal1.19 10 4 D3057 loose thermal1.08 10 5 E3057 loose thermal1.22 10 6 F3057 loose thermal1.16 10
LS精密化 シェル 解像度 : 2.4→2.46 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.316 376 - Rwork 0.261 6574 - obs - - 83.49 %
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 0.8759 0.0269 0.2149 0.914 0.0286 0.9457 0.0214 0.0401 0.1554 -0.0551 0.024 -0.2332 -0.1106 0.0123 -0.0454 0.0438 -0.0092 0.0459 -0.151 0.0058 -0.0378 49.9045 19.3027 40.0044 2 0.7335 -0.3461 -0.0778 0.7329 -0.0058 0.6746 -0.0095 -0.0686 0.0124 0.0898 0.0252 -0.0153 -0.0188 -0.0074 -0.0156 0.043 -0.0026 0.015 -0.0956 0.0088 -0.1538 32.3928 0.8369 64.8511 3 0.5231 -0.0814 -0.1332 0.9947 0.1768 0.8373 0.0382 0.0266 0.0347 0.0777 0.0634 -0.0341 -0.0412 0.1287 -0.1016 -0.1864 -0.03 -0.0114 -0.0553 -0.0204 -0.1097 72.0036 -23.0928 15.615 4 0.5898 -0.0023 -0.1307 0.8727 -0.0357 1.1701 -0.0446 -0.118 -0.0264 0.2027 0.0773 -0.1532 0.0764 0.2939 -0.0327 -0.0369 0.0548 -0.0701 0.0443 0.0098 -0.079 73.6416 -30.2852 50.5223 5 0.762 -0.2554 -0.0608 0.9029 -0.1113 0.4422 0.0158 0.1264 -0.1307 0.0632 -0.044 0.1683 0.0124 -0.1374 0.0282 -0.1755 -0.0176 -0.0258 0.0065 0.0271 -0.0934 19.1476 -15.4486 12.7533 6 0.4129 -0.0852 0.0077 0.6104 0.1342 0.9188 -0.0371 0.0307 -0.1559 0.1667 -0.0097 0.1042 0.0964 -0.0368 0.0468 -0.0621 -0.0644 0.0503 -0.0978 0.0423 0.0251 23.2949 -43.1723 34.8818
精密化 TLSグループ 大きな表を表示 (7 x 23) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA2 - 397 5 - 400 2 X-RAY DIFFRACTION 1 AG701 1 3 X-RAY DIFFRACTION 1 AL801 1 4 X-RAY DIFFRACTION 1 AR802 - 883 1 - 82 5 X-RAY DIFFRACTION 2 BB1 - 397 4 - 400 6 X-RAY DIFFRACTION 2 BH702 1 7 X-RAY DIFFRACTION 2 BM802 1 8 X-RAY DIFFRACTION 2 BS808 - 896 6 - 94 9 X-RAY DIFFRACTION 3 CC1 - 397 4 - 400 10 X-RAY DIFFRACTION 3 CI703 1 11 X-RAY DIFFRACTION 3 CN803 1 12 X-RAY DIFFRACTION 3 CT805 - 897 2 - 94 13 X-RAY DIFFRACTION 4 DD2 - 397 5 - 400 14 X-RAY DIFFRACTION 4 DJ704 1 15 X-RAY DIFFRACTION 4 DO804 1 16 X-RAY DIFFRACTION 4 DU810 - 881 6 - 77 17 X-RAY DIFFRACTION 5 EE1 - 397 4 - 400 18 X-RAY DIFFRACTION 5 EK705 1 19 X-RAY DIFFRACTION 5 EP805 1 20 X-RAY DIFFRACTION 5 EV812 - 902 7 - 97 21 X-RAY DIFFRACTION 6 FF1 - 397 4 - 400 22 X-RAY DIFFRACTION 6 FQ806 1 23 X-RAY DIFFRACTION 6 FW814 - 894 8 - 88