ソフトウェア | 名称 | バージョン | 分類 |
---|
CrystalClear | | データ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.6.4_486)精密化 | MOSFLM | | データ削減 | SCALA | | データスケーリング | PHENIX | | 位相決定 | |
|
---|
精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.55→13.669 Å / SU ML: 0.21 / σ(F): 2.01 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
---|
Rfree | 0.2355 | 4043 | 5.02 % | random |
---|
Rwork | 0.2095 | - | - | - |
---|
all | 0.2108 | 89498 | - | - |
---|
obs | 0.2108 | 80544 | 89.96 % | - |
---|
|
---|
溶媒の処理 | 減衰半径: 0.04 Å / VDWプローブ半径: 0.4 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 60.358 Å2 / ksol: 0.531 e/Å3 |
---|
原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -2.2659 Å2 | 0.2061 Å2 | 0.1216 Å2 |
---|
2- | - | 3.0403 Å2 | 0.8999 Å2 |
---|
3- | - | - | -0.7744 Å2 |
---|
|
---|
精密化ステップ | サイクル: LAST / 解像度: 1.55→13.669 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
---|
原子数 | 4856 | 0 | 22 | 352 | 5230 |
---|
|
---|
拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
---|
X-RAY DIFFRACTION | f_bond_d0.006 | 4991 | X-RAY DIFFRACTION | f_angle_d1.029 | 6747 | X-RAY DIFFRACTION | f_dihedral_angle_d12.606 | 1913 | X-RAY DIFFRACTION | f_chiral_restr0.074 | 758 | X-RAY DIFFRACTION | f_plane_restr0.004 | 880 | | | | | |
|
---|
LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
---|
1.55-1.5678 | 0.2628 | 79 | 0.2128 | 1367 | X-RAY DIFFRACTION | 46 | 1.5678-1.5869 | 0.253 | 92 | 0.2131 | 1868 | X-RAY DIFFRACTION | 64 | 1.5869-1.607 | 0.2865 | 96 | 0.2022 | 1951 | X-RAY DIFFRACTION | 67 | 1.607-1.6281 | 0.2156 | 110 | 0.2025 | 2084 | X-RAY DIFFRACTION | 70 | 1.6281-1.6504 | 0.2507 | 115 | 0.2058 | 2101 | X-RAY DIFFRACTION | 73 | 1.6504-1.6739 | 0.2141 | 103 | 0.1965 | 2267 | X-RAY DIFFRACTION | 76 | 1.6739-1.6988 | 0.2404 | 121 | 0.2039 | 2301 | X-RAY DIFFRACTION | 79 | 1.6988-1.7253 | 0.2488 | 127 | 0.1943 | 2426 | X-RAY DIFFRACTION | 82 | 1.7253-1.7536 | 0.265 | 137 | 0.2063 | 2510 | X-RAY DIFFRACTION | 86 | 1.7536-1.7837 | 0.2675 | 116 | 0.1981 | 2646 | X-RAY DIFFRACTION | 89 | 1.7837-1.8161 | 0.2694 | 160 | 0.2053 | 2680 | X-RAY DIFFRACTION | 92 | 1.8161-1.8509 | 0.249 | 148 | 0.2115 | 2766 | X-RAY DIFFRACTION | 95 | 1.8509-1.8886 | 0.2289 | 131 | 0.2027 | 2889 | X-RAY DIFFRACTION | 97 | 1.8886-1.9296 | 0.2302 | 172 | 0.211 | 2848 | X-RAY DIFFRACTION | 99 | 1.9296-1.9743 | 0.2615 | 167 | 0.2165 | 2933 | X-RAY DIFFRACTION | 99 | 1.9743-2.0236 | 0.2725 | 164 | 0.2209 | 2852 | X-RAY DIFFRACTION | 99 | 2.0236-2.0781 | 0.2466 | 128 | 0.2029 | 2900 | X-RAY DIFFRACTION | 99 | 2.0781-2.139 | 0.2303 | 151 | 0.2056 | 2972 | X-RAY DIFFRACTION | 99 | 2.139-2.2078 | 0.2387 | 150 | 0.1982 | 2860 | X-RAY DIFFRACTION | 99 | 2.2078-2.2864 | 0.2344 | 155 | 0.2044 | 2921 | X-RAY DIFFRACTION | 100 | 2.2864-2.3774 | 0.229 | 160 | 0.2078 | 2953 | X-RAY DIFFRACTION | 100 | 2.3774-2.485 | 0.2416 | 143 | 0.206 | 2941 | X-RAY DIFFRACTION | 100 | 2.485-2.6152 | 0.2558 | 142 | 0.2123 | 2951 | X-RAY DIFFRACTION | 100 | 2.6152-2.7778 | 0.2245 | 172 | 0.2214 | 2898 | X-RAY DIFFRACTION | 100 | 2.7778-2.9902 | 0.2264 | 155 | 0.2228 | 2923 | X-RAY DIFFRACTION | 100 | 2.9902-3.2873 | 0.2383 | 156 | 0.2268 | 2930 | X-RAY DIFFRACTION | 100 | 3.2873-3.7543 | 0.2109 | 155 | 0.2054 | 2924 | X-RAY DIFFRACTION | 100 | 3.7543-4.6979 | 0.2132 | 170 | 0.192 | 2921 | X-RAY DIFFRACTION | 100 | 4.6979-13.6693 | 0.2204 | 168 | 0.2275 | 2918 | X-RAY DIFFRACTION | 100 |
|
---|
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) |
---|
1 | 0.0103 | -0.018 | 0.0177 | 0.0687 | -0.0641 | 0.0606 | -0.0065 | 0.003 | -0.007 | 0.0602 | -0.0041 | 0.0067 | -0.0268 | 0.0277 | 0.0056 | 0.0415 | -0.0017 | 0.0131 | 0.0333 | 0.0025 | 0.0193 | 11.6532 | 42.9684 | 37.8675 | 2 | 0.0694 | 0.0534 | -0.0125 | 0.054 | 0.0061 | 0.0225 | 0.0241 | 0.0075 | 0.0593 | 0.0228 | -0.0199 | 0.0295 | -0.0119 | 0.0027 | -0.0014 | 0.0129 | 0.0038 | -0.0003 | 0.0263 | -0.0022 | 0.0371 | 8.0256 | 46.4082 | 28.6839 | 3 | 0.1897 | -0.095 | -0.2383 | 0.0907 | 0.1238 | 0.3808 | -0.0419 | 0.0184 | -0.0101 | 0.0307 | -0.0168 | 0.0085 | 0.047 | -0.0318 | 0.0398 | 0.0076 | 0.0003 | -0.006 | 0.0068 | -0.0015 | -0.0073 | 13.1712 | 38.6603 | 17.1654 | 4 | 0.3689 | 0.0466 | -0.0087 | 0.017 | 0.0405 | 0.1642 | 0.0045 | 0.0071 | 0.0926 | -0.0081 | -0.0025 | 0.0035 | -0.0246 | 0.0229 | -0.0022 | 0.0208 | 0.0014 | 0.0017 | 0.0062 | 0.0014 | 0.0194 | 20.6856 | 51.9771 | 19.2901 | 5 | 0.0527 | 0.0058 | -0.0449 | 0.0415 | -0.0172 | 0.0424 | -0.0031 | 0.0271 | 0.0037 | -0.0089 | -0.0044 | 0.0239 | 0.0067 | -0.0259 | -0.0069 | -0.01 | -0.0129 | -0.0049 | 0.0146 | 0.008 | 0.0177 | 22.4983 | 44.1057 | 11.039 | 6 | 0.0293 | -0.0044 | -0.0004 | 0.011 | -0.014 | 0.0266 | 0.0217 | 0.0118 | -0.0761 | 0.014 | -0.0243 | 0.0121 | 0.0115 | 0.0077 | -0.0004 | 0.0621 | 0.0078 | -0.0255 | 0.0189 | -0.0203 | 0.0583 | 34.6607 | 33.6451 | 17.6725 | 7 | 0.0107 | -0.0249 | 0.0118 | 0.1459 | -0.0602 | 0.0519 | -0.0029 | 0.0134 | 0.0122 | 0.0054 | -0.0372 | -0.0613 | -0.0137 | 0.0298 | 0.015 | -0.029 | -0.0388 | 0.0209 | -0.0379 | 0.0263 | -0.0133 | 33.464 | 46.9153 | 10.5042 | 8 | 0.1352 | -0.0154 | 0.0309 | 0.1068 | 0.058 | 0.134 | -0.0061 | 0.0513 | 0.0213 | 0.0219 | 0.019 | -0.0256 | 0.0516 | 0.017 | -0.0146 | 0.0208 | 0.0026 | -0.0005 | 0.0193 | 0.003 | 0.027 | 31.3906 | 16.0575 | -1.4753 | 9 | 0.019 | 0.014 | 0.0049 | 0.0712 | 0.0076 | 0.1258 | -0.0054 | -0.008 | -0.0028 | 0.0012 | -0.0172 | -0.0095 | -0.0432 | 0.0285 | 0.0161 | 0.022 | 0.0015 | 0.0078 | 0.0087 | 0.006 | 0.0177 | 28.0979 | 25.7239 | -14.5823 | 10 | 0.1266 | 0.0319 | 0.0296 | 0.0096 | 0.0097 | 0.0087 | 0.0043 | 0.0279 | -0.0357 | 0.0031 | 0.0026 | -0.0021 | 0.0062 | 0.0034 | -0.0127 | -0.0303 | 0.0084 | -0.0194 | -0.0147 | -0.0202 | -0.0209 | 17.5754 | 19.8665 | -16.5964 | 11 | 0.04 | -0.05 | 0.0063 | 0.1533 | 0.0627 | 0.0559 | 0.0134 | 0.0291 | 0.0107 | -0.0007 | -0.0053 | -0.0445 | -0.0049 | -0.0234 | -0.0116 | -0.0102 | -0.0034 | -0 | 0.022 | -0.0034 | -0.0024 | 18.5832 | 31.5678 | -18.1023 | 12 | 0.0606 | -0.0323 | -0.0309 | 0.018 | 0.0113 | 0.0486 | 0.0126 | -0.0407 | 0.0686 | -0.0028 | 0.008 | -0.023 | -0.0201 | -0.0039 | -0.0204 | 0.0613 | -0.0094 | 0.0236 | 0.0423 | -0.0303 | 0.0708 | 7.8271 | 35.267 | -7.3141 | 13 | 0.0128 | 0.0162 | 0.0466 | 0.0531 | 0.1099 | 0.2486 | -0.0073 | -0.0022 | 0.0095 | -0.0243 | -0.027 | 0.0045 | -0.0445 | -0.0859 | -0.0062 | -0.0242 | 0.0299 | -0.0163 | 0.0054 | 0.0104 | -0.03 | 8.6368 | 32.2788 | -19.2818 | 14 | 0.0167 | 0.0012 | 0.0001 | 0.0055 | -0.0048 | 0.0121 | 0.013 | 0.0001 | -0.0209 | 0.0062 | 0.0086 | -0.0032 | 0.02 | -0.0314 | -0.0175 | -0.0058 | -0.013 | -0.0242 | 0.0853 | -0.0169 | 0.0037 | 3.8444 | 23.1221 | -25.789 |
|
---|
精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
---|
1 | X-RAY DIFFRACTION | 1 | (chain A and resid 2:48)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 49:91)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 92:121)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 122:160)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 161:192)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 193:223)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 224:307)8 | X-RAY DIFFRACTION | 8 | (chain B and resid 2:82)9 | X-RAY DIFFRACTION | 9 | (chain B and resid 83:130)10 | X-RAY DIFFRACTION | 10 | (chain B and resid 131:162)11 | X-RAY DIFFRACTION | 11 | (chain B and resid 163:192)12 | X-RAY DIFFRACTION | 12 | (chain B and resid 193:225)13 | X-RAY DIFFRACTION | 13 | (chain B and resid 226:281)14 | X-RAY DIFFRACTION | 14 | (chain B and resid 282:307) | | | | | | | | | | | | | |
|
---|