ソフトウェア 名称 バージョン 分類 NB DENZOデータ削減 Show SCALEPACKデータスケーリング Show SHARP位相決定 Show 直接法5 位相決定 Show REFMAC5.2.0019精密化 Show PDB_EXTRACT3 データ抽出 Show MAR345CCDデータ収集 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 : 単波長異常分散 / 解像度 : 3.344→47.168 Å / Cor.coef. Fo :Fc : 0.952 / Cor.coef. Fo :Fc free : 0.95 / WRfactor Rfree : 0.286 / WRfactor Rwork : 0.232 / SU B : 58.864 / SU ML : 0.398 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0 / ESU R Free : 0.452 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.252 648 4.941 % RANDOM Rwork 0.215 - - - obs 0.217 13115 99.101 % -
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 BULK SOLVENT原子変位パラメータ Biso mean : 74.648 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.209 Å2 0.604 Å2 0 Å2 2- - 1.209 Å2 0 Å2 3- - - -1.813 Å2
精密化ステップ サイクル : LAST / 解像度 : 3.344→47.168 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3437 0 0 0 3437
拘束条件 大きな表を表示 (5 x 17) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.006 0.022 3501 X-RAY DIFFRACTION r_angle_refined_deg0.904 1.942 4710 X-RAY DIFFRACTION r_dihedral_angle_1_deg4.917 5 413 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.599 25.187 187 X-RAY DIFFRACTION r_dihedral_angle_3_deg19.415 15 686 X-RAY DIFFRACTION r_dihedral_angle_4_deg17.282 15 20 X-RAY DIFFRACTION r_chiral_restr0.074 0.2 501 X-RAY DIFFRACTION r_gen_planes_refined0.002 0.02 2632 X-RAY DIFFRACTION r_nbd_refined0.213 0.2 1729 X-RAY DIFFRACTION r_nbtor_refined0.297 0.2 2390 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.121 0.2 92 X-RAY DIFFRACTION r_symmetry_vdw_refined0.175 0.2 62 X-RAY DIFFRACTION r_symmetry_hbond_refined0.194 0.2 5 X-RAY DIFFRACTION r_mcbond_it0.216 1.5 2115 X-RAY DIFFRACTION r_mcangle_it0.385 2 3348 X-RAY DIFFRACTION r_scbond_it0.38 3 1554 X-RAY DIFFRACTION r_scangle_it0.642 4.5 1362
Refine LS restraints NCS Dom-ID : 1 / Auth asym-ID : A / Ens-ID : 1 / 数 : 1696 / Refine-ID : X-RAY DIFFRACTION
タイプ Rms dev position (Å)Weight position MEDIUM POSITIONAL0.48 0.5 MEDIUM THERMAL0.14 2
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 20
大きな表を表示 (7 x 20) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)3.344-3.431 0.4 47 0.36 885 955 97.592 3.431-3.525 0.298 42 0.316 847 891 99.776 3.525-3.627 0.385 56 0.278 844 901 99.889 3.627-3.738 0.283 36 0.27 833 869 100 3.738-3.86 0.281 38 0.25 803 842 99.881 3.86-3.996 0.24 38 0.234 789 827 100 3.996-4.146 0.28 45 0.221 758 804 99.876 4.146-4.315 0.271 30 0.211 723 754 99.867 4.315-4.506 0.279 32 0.214 699 735 99.456 4.506-4.725 0.261 37 0.209 676 717 99.442 4.725-4.98 0.206 38 0.18 653 697 99.139 4.98-5.28 0.214 30 0.186 611 647 99.073 5.28-5.643 0.366 28 0.24 589 624 98.878 5.643-6.092 0.44 30 0.246 525 562 98.754 6.092-6.669 0.263 31 0.258 496 534 98.689 6.669-7.449 0.299 27 0.221 454 490 98.163 7.449-8.588 0.223 19 0.178 430 458 98.035 8.588-10.485 0.116 22 0.136 367 390 99.744 10.485-14.689 0.239 13 0.164 302 319 98.746 14.689-47.168 0.196 9 0.312 183 218 88.073
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 24) 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 0.6272 -2.4505 0.6804 19.934 -14.5543 14.3977 0.1787 -1.1574 0.2568 -0.6744 -0.1546 0.2186 -0.9406 0.4849 -0.0241 0.8689 0.0133 -0.035 0.1894 0.2534 0.5001 3.3023 70.7933 -7.8481 2 0.4745 -3.1867 1.4626 29.9726 -21.5058 20.4321 -0.268 -0.3865 -0.3169 0.0572 0.2573 -1.5633 -0.0478 0.4478 0.0106 0.5094 0.1201 -0.1674 0.1618 0.4272 0.5403 5.3161 48.1636 5.5501 3 9.0656 -6.6805 9.7257 40.7192 -41.3651 43.1052 -0.9104 -0.0599 -0.2608 -1.9582 0.3109 -1.2565 2.2734 0.085 0.5995 0.9242 0.3561 0.0315 0.2625 0.2767 0.3516 6.3667 25.9749 24.1063 4 3.242 -5.3865 9.0654 8.9496 -15.0619 25.3488 -0.8545 -1.3323 -2.3293 -1.366 2.3689 0.2759 3.894 -1.8027 -1.5144 1.0896 0.0087 -0.4073 1.1703 0.4158 1.7095 2.1959 12.681 33.404 5 5.6987 -3.2944 9.8639 13.8465 -24.4464 46.4941 0.0693 1.0824 -0.8359 -2.0822 0.19 -0.8547 3.0423 -0.9496 -0.2593 1.4045 0.1283 -0.3305 0.3497 0.3386 0.8126 -0.7871 26.4147 12.4395 6 50.8988 10.6195 -1.8751 3.2842 8.2116 69.3255 -0.4838 2.8745 -1.9406 -2.1772 0.8165 -1.9479 2.1805 -1.3444 -0.3327 1.1611 0.0945 -0.0728 0.0128 0.4399 0.664 0.6934 43.7034 -4.3383 7 33.9923 29.7755 4.6433 32.7809 -18.4049 76.0164 0.4126 4.3875 -3.8331 -3.3957 0.1438 -1.9344 2.9259 1.077 -0.5564 1.1768 0.477 -0.0509 0.0736 0.3001 0.476 5.192 54.2929 -9.6089 8 3.6482 8.5574 -6.0329 32.8098 -21.6849 15.2735 -0.3503 0.4615 -0.3378 -1.1283 0.187 -2.0258 0.8619 0.6365 0.1633 0.7089 0.0152 0.1203 0.4118 0.3187 0.7073 12.8343 80.9018 -23.1126 9 12.5107 7.9261 2.3186 21.5563 -5.0891 9.1298 -0.2946 1.6389 -0.1322 -0.8773 1.7164 0.4703 0.1019 -0.9147 -1.4217 1.0097 -0.025 0.127 0.4113 0.2694 0.3896 6.3898 82.9367 -28.0091 10 10.9505 13.9449 -14.3227 40.3459 -30.8256 26.5327 -0.7559 1.0578 0.3116 -1.5507 1.7589 1.3398 0.3206 -2.4606 -1.0029 0.8174 -0.1122 -0.1072 0.285 0.3 0.4517 -1.8982 65.3409 -13.863 11 2.876 0.6151 0.7546 13.0998 -11.055 9.8991 -0.3625 0.5235 0.0308 -0.9121 0.6481 -0.3338 0.6134 -0.5394 -0.2856 0.7989 -0.0256 -0.225 0.2599 0.4485 0.4262 -6.1517 44.5149 5.574 12 13.3594 -0.0503 -16.8167 4.474 -5.2922 31.4671 -0.4015 -2.1488 0.173 -0.3327 0.2856 1.9918 1.6107 -0.8875 0.1159 0.9211 -0.3279 -0.3383 0.5035 0.6471 0.7948 -9.6701 24.479 27.8543 13 3.0971 -0.9805 2.8147 15.8047 -3.2225 2.9088 -0.857 1.6085 -0.2193 -0.7273 0.0008 -0.9165 0.1189 1.9206 0.8562 1.2962 0.7901 -0.0079 0.6276 0.384 0.6825 19.3568 8.6349 45.6626 14 2.0054 2.1382 2.0222 8.8662 -6.3859 13.1172 -0.6036 0.3156 1.4642 0.0692 0.347 -1.5923 0.3581 1.2316 0.2566 0.5703 0.2465 -0.0019 0.2729 0.3659 0.6828 11.4389 27.5102 33.8934 15 2.989 -6.133 7.1452 12.6356 -14.0583 24.1745 -0.9894 -0.2259 0.7169 -0.4117 1.0899 -0.7812 -0.3226 0.2859 -0.1006 0.6503 0.0002 -0.1785 0.2925 0.371 0.4576 0.7048 47.7086 15.63 16 0.0006 0.1325 -0.0548 31.8152 -13.1585 5.4422 0.6604 -1.1176 2.4515 -0.8734 1.6622 1.0123 -1.4314 -1.7472 -2.3226 1.0244 -0.0031 -0.0272 1.5309 0.3441 0.9719 -9.7456 58.6984 4.6116 17 4.2897 -6.9689 12.1583 11.7715 -21.4691 41.01 -0.4143 -0.5831 0.91 1.3513 0.7206 0.3659 -1.0632 -2.1367 -0.3063 0.6361 0.1764 0.045 0.4116 0.5068 0.7756 -5.5737 45.5369 25.5521 18 19.8937 -4.9836 8.225 29.4317 -9.3687 33.6849 -0.7195 -1.3307 2.4065 1.2849 0.7112 -0.599 -0.5648 -1.3036 0.0083 0.6689 0.2706 -0.1682 0.1182 0.2774 0.5098 4.5925 29.9232 42.4896 19 15.5979 -16.7306 12.6983 20.175 -12.7378 10.6871 -0.3503 -0.5703 1.0195 0.1264 0.2601 -1.4101 -0.6002 0.2122 0.0902 0.9069 0.3493 -0.1529 0.4878 0.38 0.7275 29.2174 8.0818 58.4315 20 30.7771 -19.9449 16.6447 20.2321 -12.431 9.3718 1.0402 -0.7171 -0.5461 -0.8228 -0.1992 -0.2538 -0.2115 0.1671 -0.841 1.2627 0.4172 -0.2355 1.0679 0.2279 0.5447 28.62 -0.0691 66.3535 21 24.5345 -17.4311 20.9253 26.2065 -28.9142 32.1233 0.6675 -2.1739 -0.9688 -1.4192 1.0748 1.5944 2.4307 -2.0908 -1.7423 1.045 0.3429 -0.1296 0.3903 0.2025 0.5611 11.9359 11.248 51.635 22 14.5637 -9.7269 9.4642 11.7932 -13.5143 16.946 -0.1706 -1.0201 -0.0385 -0.0823 1.1507 0.0965 0.9913 -1.3881 -0.9801 0.6876 0.0358 -0.11 0.1629 0.3146 0.2963 -0.9383 26.2245 33.2724 23 15.7592 -6.7557 6.2656 6.9123 -1.0317 3.1724 -0.5901 0.6482 0.0219 -1.8851 0.3188 0.8934 1.322 -3.7235 0.2713 0.7586 -0.1843 -0.1818 0.835 0.5656 0.6372 -13.7641 42.6622 12.1413 24 42.996 -7.7998 4.6846 1.415 -0.8498 0.5104 -2.2458 -1.5276 -1.7059 2.0775 -0.0743 0.6033 -2.4692 -1.8226 2.3202 2.3479 -0.5726 0.0122 1.8474 0.517 0.9887 -12.7277 37.5646 -3.1615
精密化 TLSグループ 大きな表を表示 (7 x 24) 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 AA12 - 23 15 - 26 2 X-RAY DIFFRACTION 2 AA24 - 46 27 - 49 3 X-RAY DIFFRACTION 3 AA47 - 60 50 - 63 4 X-RAY DIFFRACTION 4 AA61 - 72 64 - 75 5 X-RAY DIFFRACTION 5 AA73 - 97 76 - 100 6 X-RAY DIFFRACTION 6 AA98 - 106 101 - 109 7 X-RAY DIFFRACTION 7 AA107 - 114 110 - 117 8 X-RAY DIFFRACTION 8 AA115 - 147 118 - 150 9 X-RAY DIFFRACTION 9 AA148 - 162 151 - 165 10 X-RAY DIFFRACTION 10 AA163 - 177 166 - 180 11 X-RAY DIFFRACTION 11 AA178 - 201 181 - 204 12 X-RAY DIFFRACTION 12 AA202 - 216 205 - 219 13 X-RAY DIFFRACTION 13 BB12 - 23 15 - 26 14 X-RAY DIFFRACTION 14 BB24 - 44 27 - 47 15 X-RAY DIFFRACTION 15 BB45 - 60 48 - 63 16 X-RAY DIFFRACTION 16 BB61 - 72 64 - 75 17 X-RAY DIFFRACTION 17 BB73 - 97 76 - 100 18 X-RAY DIFFRACTION 18 BB98 - 107 101 - 110 19 X-RAY DIFFRACTION 19 BB108 - 146 111 - 149 20 X-RAY DIFFRACTION 20 BB147 - 163 150 - 166 21 X-RAY DIFFRACTION 21 BB164 - 177 167 - 180 22 X-RAY DIFFRACTION 22 BB178 - 199 181 - 202 23 X-RAY DIFFRACTION 23 BB200 - 216 203 - 219 24 X-RAY DIFFRACTION 24 BB217 - 221 220 - 224