ソフトウェア | 名称 | バージョン | 分類 |
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XSCALE | | データスケーリング | PHASER | 2.7.17位相決定 | PHENIX | 1.11.1_2575精密化 | PDB_EXTRACT | 3.24 | データ抽出 | XDS | | データ削減 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4H9U 解像度: 1.726→19.986 Å / SU ML: 0.21 / 交差検証法: THROUGHOUT / σ(F): 0.91 / 位相誤差: 26.49
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2639 | 12924 | 4.9 % |
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Rwork | 0.2187 | - | - |
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obs | 0.221 | 133282 | 92.9 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å |
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原子変位パラメータ | Biso max: 84.32 Å2 / Biso mean: 30.5855 Å2 / Biso min: 3.55 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.726→19.986 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 10152 | 0 | 28 | 762 | 10942 |
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Biso mean | - | - | 34.84 | 33.14 | - |
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残基数 | - | - | - | - | 1292 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.012 | 10439 | X-RAY DIFFRACTION | f_angle_d0.91 | 14081 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 1517 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1863 | X-RAY DIFFRACTION | f_dihedral_angle_d4.012 | 6208 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.7257-1.7453 | 0.453 | 23 | 0.3774 | 467 | 490 | 5 | 1.7453-1.7659 | 0.3571 | 315 | 0.2696 | 6243 | 6558 | 69 | 1.7659-1.7874 | 0.2902 | 387 | 0.2375 | 8573 | 8960 | 96 | 1.7874-1.81 | 0.2779 | 440 | 0.2182 | 8707 | 9147 | 96 | 1.81-1.8338 | 0.273 | 355 | 0.2246 | 8697 | 9052 | 95 | 1.8338-1.8589 | 0.2954 | 479 | 0.24 | 8550 | 9029 | 96 | 1.8589-1.8854 | 0.2846 | 460 | 0.2436 | 8704 | 9164 | 96 | 1.8854-1.9135 | 0.3066 | 475 | 0.2405 | 8510 | 8985 | 96 | 1.9135-1.9434 | 0.2779 | 474 | 0.2252 | 8651 | 9125 | 96 | 1.9434-1.9753 | 0.2645 | 476 | 0.2296 | 8537 | 9013 | 95 | 1.9753-2.0093 | 0.2847 | 543 | 0.2228 | 8733 | 9276 | 97 | 2.0093-2.0458 | 0.2684 | 490 | 0.2268 | 8575 | 9065 | 96 | 2.0458-2.0851 | 0.2828 | 462 | 0.2317 | 8563 | 9025 | 97 | 2.0851-2.1276 | 0.2586 | 551 | 0.2222 | 8812 | 9363 | 96 | 2.1276-2.1738 | 0.2966 | 445 | 0.2253 | 8532 | 8977 | 97 | 2.1738-2.2243 | 0.2879 | 434 | 0.2284 | 8862 | 9296 | 96 | 2.2243-2.2799 | 0.2842 | 405 | 0.2277 | 8633 | 9038 | 97 | 2.2799-2.3414 | 0.2621 | 424 | 0.2201 | 8849 | 9273 | 97 | 2.3414-2.4102 | 0.2609 | 423 | 0.2176 | 8709 | 9132 | 97 | 2.4102-2.4879 | 0.2792 | 421 | 0.2217 | 8774 | 9195 | 97 | 2.4879-2.5766 | 0.2683 | 384 | 0.2274 | 8856 | 9240 | 97 | 2.5766-2.6795 | 0.2521 | 506 | 0.2305 | 8779 | 9285 | 97 | 2.6795-2.8012 | 0.2944 | 455 | 0.2344 | 8760 | 9215 | 98 | 2.8012-2.9484 | 0.2637 | 430 | 0.231 | 8815 | 9245 | 98 | 2.9484-3.1325 | 0.2825 | 486 | 0.217 | 8750 | 9236 | 98 | 3.1325-3.3733 | 0.2683 | 350 | 0.2131 | 8993 | 9343 | 98 | 3.3733-3.7108 | 0.2387 | 479 | 0.2038 | 8789 | 9268 | 98 | 3.7108-4.2433 | 0.2237 | 463 | 0.1963 | 8852 | 9315 | 98 | 4.2433-5.3293 | 0.2144 | 425 | 0.189 | 8816 | 9241 | 99 | 5.3293-19.9872 | 0.2653 | 464 | 0.2189 | 8806 | 9270 | 98 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION 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) |
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1 | 0.0009 | -0.0003 | -0.0015 | 0.0572 | 0.0315 | 0.0266 | -0.0362 | 0.0032 | 0.055 | 0.0394 | 0.0256 | 0.002 | 0.0172 | 0.0225 | -0.0219 | 0.0296 | 0.0097 | -0.0094 | 0.0572 | -0.0306 | 0.1464 | 28.7153 | 51.1055 | 26.3397 | 2 | 0.0608 | -0.0579 | 0.0891 | 0.0579 | -0.0619 | 0.1495 | 0.0571 | -0.0675 | 0.042 | 0.0116 | 0.0366 | 0.0336 | -0.0051 | 0.0289 | 0.0431 | 0.04 | -0.0204 | 0.0446 | 0.1121 | -0.0187 | 0.0539 | 15.1371 | 36.9016 | 29.7649 | 3 | 0.0011 | -0.0025 | -0.0102 | 0.0149 | 0.0041 | 0.0445 | 0.026 | -0.0389 | 0.0647 | 0.0075 | 0.0061 | 0.0146 | -0.0266 | -0.0308 | 0.0059 | 0.0484 | 0.0069 | 0.0115 | 0.06 | -0.0189 | 0.1289 | 20.784 | 44.5171 | 25.2225 | 4 | 0.0437 | -0.0243 | 0.0315 | 0.0455 | -0.0785 | 0.1455 | -0.0017 | -0.0303 | 0.0468 | -0.0328 | -0.027 | -0.0004 | 0.0691 | -0.0086 | -0.0051 | 0.0261 | 0.0049 | -0.0029 | 0.0209 | 0.0164 | 0.0755 | 27.2269 | 36.3376 | 20.1251 | 5 | -0.0004 | -0.0006 | 0.001 | 0.0038 | -0.0023 | -0.0006 | -0.0342 | -0.02 | -0.015 | -0.0368 | 0.0004 | -0.0442 | 0.0124 | 0.002 | 0 | 0.0857 | 0.005 | 0.0083 | 0.0653 | 0.0204 | 0.0413 | 29.3158 | 35.4081 | 5.4405 | 6 | 0.0075 | 0.0016 | -0.0083 | 0.0017 | 0.0035 | 0.0209 | -0.0121 | 0.0193 | 0.0222 | -0.0383 | 0.0397 | 0.0233 | 0.0291 | -0.0009 | 0.0014 | 0.0565 | 0.0051 | 0.0005 | 0.0422 | 0.0075 | 0.1053 | 29.7897 | 38.3102 | 16.3014 | 7 | 0.0073 | -0.0011 | -0.0001 | 0.0031 | -0.0007 | 0.0023 | 0.0149 | 0.0054 | 0.0279 | 0.0089 | 0.0037 | 0.0111 | 0.0032 | 0.0106 | 0.0219 | 0.0129 | 0.0456 | 0.0628 | 0.0193 | 0.0264 | 0.0648 | 37.427 | 37.168 | 10.1846 | 8 | 0.0043 | 0.0053 | 0.0047 | 0.0492 | 0.0363 | 0.0273 | 0.0346 | -0.0767 | 0.0586 | -0.0536 | 0.0132 | -0.0652 | 0.0172 | 0.077 | 0.004 | 0.0393 | 0.0136 | -0.0053 | 0.0875 | -0.0035 | 0.1107 | 43.5548 | 36.1847 | 23.9292 | 9 | 0.0045 | 0.0005 | -0.0037 | 0.0031 | -0.0044 | 0.006 | 0.0137 | -0.0133 | -0.0301 | 0.032 | 0.0477 | 0.0102 | 0.022 | 0.0207 | 0.0089 | 0.1556 | -0.0123 | -0.0402 | 0.2468 | 0.0338 | 0.0567 | 38.9076 | 31.9495 | 38.6254 | 10 | 0.077 | -0.0593 | 0.008 | 0.0396 | -0.0066 | 0.0042 | -0.0577 | -0.161 | 0.0723 | 0.052 | 0.0495 | -0.0461 | -0.014 | -0.0145 | -0.0188 | 0.0915 | -0.0016 | 0.0003 | 0.149 | -0.0209 | 0.0695 | 32.8181 | 39.0198 | 37.6306 | 11 | 0.0084 | 0.0079 | -0.0037 | 0.0129 | -0.0109 | 0.0263 | 0.025 | 0.0194 | 0.0066 | -0.0463 | 0.0335 | 0.0481 | -0.0063 | -0.0222 | 0.0277 | 0.0792 | 0.0026 | -0.0354 | 0.0653 | 0.002 | 0.1333 | -2.5326 | 16.1049 | 3.6508 | 12 | 0.0182 | -0.0161 | 0.0142 | 0.0187 | -0.0134 | 0.0054 | 0.0329 | 0.0102 | -0.006 | -0.0521 | -0.0067 | 0.0503 | -0.0175 | -0.0029 | 0.039 | 0.0966 | 0.0504 | -0.0625 | -0.0368 | 0.0733 | -0.0001 | 10.0211 | 31.2337 | 0.2945 | 13 | 0.0267 | 0.0032 | -0.019 | 0.0045 | 0.003 | 0.0209 | 0.028 | 0.0194 | 0.0081 | -0.0647 | 0.0055 | 0.0545 | -0.0437 | 0.0185 | 0.0056 | 0.0699 | -0.0037 | -0.0192 | 0.0534 | 0.009 | 0.0723 | 6.5152 | 22.6756 | 6.7985 | 14 | 0.0041 | -0.0014 | -0.0049 | 0.0031 | 0.0024 | 0.0039 | 0.0155 | -0.0412 | -0.0108 | 0.0043 | -0.0228 | -0.0312 | -0.0088 | 0.0084 | -0 | 0.0661 | -0.0037 | 0.0085 | 0.0704 | 0.0195 | 0.0976 | 13.1251 | 17.1958 | 24.5812 | 15 | 0.0059 | -0.0111 | 0.0197 | 0.0159 | -0.0133 | 0.0192 | 0.0304 | -0.0013 | -0.0521 | -0.0225 | 0.0182 | 0.0389 | 0.0329 | -0.0061 | 0.0409 | -0.0126 | 0.1283 | -0.0576 | -0.1969 | 0.1475 | 0.0369 | 12.717 | 10.0456 | 14.4101 | 16 | 0.0335 | -0.0178 | 0.007 | 0.016 | -0.0027 | 0.0137 | 0.0446 | 0.004 | -0.0464 | -0.0902 | -0.0092 | 0.0378 | 0.0379 | 0.0015 | 0.0219 | 0.0901 | 0.01 | -0.0113 | 0.0579 | 0.0021 | 0.1014 | 13.7463 | 3.7369 | 1.395 | 17 | 0.011 | -0.0065 | 0.0083 | 0.0151 | -0.0083 | 0.0064 | 0.018 | 0.0138 | -0.0046 | -0.0081 | -0.0038 | -0.0158 | 0.024 | 0.0022 | -0.0047 | 0.2392 | 0.0655 | -0.0214 | 0.1956 | -0.0743 | 0.1538 | 17.6275 | 5.9004 | -9.4654 | 18 | 0.0564 | -0.012 | 0.0395 | 0.0208 | 0.0067 | 0.0343 | 0.0527 | 0.0901 | -0.0358 | -0.0869 | -0.0401 | -0.0154 | 0.0385 | 0.0657 | 0.0122 | 0.1867 | 0.0244 | -0.0256 | 0.1454 | 0.0003 | 0.0619 | 13.0911 | 15.764 | -8.6722 | 19 | 0.0025 | 0.0034 | 0.0002 | 0.0022 | 0.0004 | -0.0001 | 0.0258 | -0.0078 | -0.0225 | -0.0305 | -0.003 | 0.0187 | -0.0021 | -0.0092 | 0.0034 | 0.1485 | 0.0087 | -0.0637 | 0.0759 | -0.0194 | 0.1404 | -0.7691 | 5.5934 | -3.6863 | 20 | 0.0054 | 0.0112 | -0.0051 | 0.0108 | -0.0053 | 0.0136 | 0.0106 | 0.0292 | -0.0721 | -0.0415 | 0.0264 | -0.0193 | 0.0488 | -0.0231 | -0 | 0.2752 | -0.0325 | 0.0185 | 0.3376 | -0.0517 | 0.2931 | 2.2786 | 0.2274 | 69.4076 | 21 | 0.011 | -0.0046 | -0.0073 | 0.0067 | 0.009 | 0.0083 | -0.039 | 0.0469 | -0.0266 | 0.0169 | -0.0273 | -0.0096 | -0.0274 | 0.0593 | 0 | 0.2526 | -0.0272 | 0.0119 | 0.3206 | -0.0551 | 0.2886 | 16.0889 | 9.2769 | 79.9529 | 22 | 0.0078 | 0.0021 | -0.0059 | 0.0056 | -0.0017 | 0.0076 | 0.0052 | 0.0032 | -0.0088 | -0.0684 | -0.002 | 0.0178 | -0.0061 | 0.0101 | 0 | 0.239 | -0.0522 | 0.0236 | 0.3972 | -0.0061 | 0.2787 | 19.3015 | 12.9183 | 60.4305 | 23 | 0.0037 | -0.0028 | -0.0048 | 0.0066 | -0.0093 | 0.0087 | -0.0609 | 0.032 | 0.0428 | -0.0475 | -0.0475 | 0.0901 | 0.0278 | 0.0065 | 0 | 0.24 | -0.0327 | 0.0316 | 0.3566 | -0.0745 | 0.2517 | 8.2455 | 6.558 | 55.4983 | 24 | 0.0034 | -0.0006 | -0.0059 | -0.001 | -0.001 | 0.0081 | 0.0357 | -0.052 | -0.031 | -0.0038 | 0.0609 | -0.0449 | 0.0695 | -0.0305 | 0 | 0.3282 | -0.0283 | 0.0119 | 0.2992 | 0.0182 | 0.25 | -5.2131 | 15.6678 | 100.2923 | 25 | 0.0084 | -0.0076 | 0.0068 | 0.0081 | -0.001 | 0.0064 | 0.0092 | 0.0361 | -0.0185 | -0.0142 | -0.0368 | 0.014 | 0.0175 | 0.0206 | -0 | 0.2522 | -0.025 | 0.0236 | 0.3263 | -0.0749 | 0.2756 | -6.3998 | 18.2204 | 95.0385 | 26 | 0.0084 | -0.0114 | -0.0039 | 0.0183 | -0.015 | 0.0148 | 0.0544 | 0.0206 | 0.0093 | 0.0076 | 0.0052 | -0.0013 | -0.1259 | -0.0577 | -0 | 0.2541 | 0.0005 | 0.0217 | 0.3216 | -0.0359 | 0.2633 | -6.3167 | 31.9127 | 86.1682 | 27 | 0.0001 | 0.0004 | -0.0006 | 0.001 | -0.0015 | 0.0026 | 0.0419 | -0.0092 | 0.0241 | 0.0181 | -0.0047 | -0.0009 | -0.0359 | 0.0076 | -0 | 0.2976 | -0.007 | 0.0135 | 0.2716 | -0.0938 | 0.2796 | 4.6095 | 35.2078 | 103.8738 | 28 | 0.003 | 0.0031 | -0.0043 | 0.0024 | -0.0041 | 0.0048 | -0.0429 | 0.0271 | -0.0039 | 0.0003 | 0.0006 | -0.0071 | -0.0389 | 0.0102 | 0 | 0.3487 | 0.0136 | 0.0851 | 0.3091 | -0.0271 | 0.2737 | -1.6678 | 30.56 | 103.3007 | 29 | 0.0035 | 0.0035 | 0.0022 | 0.0104 | -0.0057 | 0.0069 | 0.0115 | -0.008 | 0.0044 | 0.0666 | -0.0582 | -0.0239 | -0.0257 | 0.0415 | -0 | 0.2165 | -0.031 | 0.0232 | 0.2589 | -0.016 | 0.1874 | 1.5234 | 28.0265 | 109.0156 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 3 through 26 )A3 - 26 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 27 through 61 )A27 - 61 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 62 through 88 )A62 - 88 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 89 through 106 )A89 - 106 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 107 through 131 )A107 - 131 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 132 through 154 )A132 - 154 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 155 through 171 )A155 - 171 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 172 through 228 )A172 - 228 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 229 through 254 )A229 - 254 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 255 through 325 )A255 - 325 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 3 through 26 )B3 - 26 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 27 through 61 )B27 - 61 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 62 through 106 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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