Software | Name | Version | Classification |
---|
XSCALE | | data scalingCoot | | model buildingPHENIX | | refinementPDB_EXTRACT | 3.22 | data extractionXDS | | data reductionMOLREP | | phasing | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4nbv Resolution: 1.65→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.09
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.2077 | 1973 | 1.63 % |
---|
Rwork | 0.1752 | - | - |
---|
obs | 0.1757 | 121308 | 99.19 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
---|
Displacement parameters | Biso max: 70.9 Å2 / Biso mean: 23.0859 Å2 / Biso min: 8.15 Å2 |
---|
Refinement step | Cycle: final / Resolution: 1.65→50 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 7668 | 0 | 48 | 1057 | 8773 |
---|
Biso mean | - | - | 35.24 | 33.24 | - |
---|
Num. residues | - | - | - | - | 1054 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.006 | 8004 | X-RAY DIFFRACTION | f_angle_d0.811 | 10890 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 1274 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1449 | X-RAY DIFFRACTION | f_dihedral_angle_d17.358 | 4846 | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 % Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork |
---|
1.65-1.6912 | 0.2896 | 116 | 0.2275 | 8455 | 1.6912-1.7369 | 0.2447 | 170 | 0.2147 | 8482 | 1.7369-1.7881 | 0.2226 | 147 | 0.1986 | 8504 | 1.7881-1.8458 | 0.2171 | 152 | 0.1926 | 8449 | 1.8458-1.9117 | 0.2284 | 145 | 0.1907 | 8491 | 1.9117-1.9883 | 0.2431 | 140 | 0.1888 | 8500 | 1.9883-2.0788 | 0.2087 | 143 | 0.1772 | 8559 | 2.0788-2.1884 | 0.1973 | 122 | 0.1739 | 8492 | 2.1884-2.3255 | 0.2073 | 168 | 0.1691 | 8537 | 2.3255-2.505 | 0.2063 | 134 | 0.1688 | 8547 | 2.505-2.7571 | 0.2211 | 122 | 0.1747 | 8562 | 2.7571-3.1559 | 0.2078 | 105 | 0.1686 | 8551 | 3.1559-3.9758 | 0.207 | 169 | 0.163 | 8549 | 3.9758-50 | 0.1715 | 140 | 0.1682 | 8657 |
|
---|
Refinement TLS params. | Method: 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 | 2.2352 | 0.5026 | 0.2186 | 3.7424 | 1.308 | 2.1017 | -0.0024 | 0.078 | -0.0272 | -0.1131 | -0.0126 | -0.3959 | 0.0687 | 0.1187 | 0.0131 | 0.1819 | -0.0194 | 0.0592 | 0.1096 | 0.0401 | 0.1783 | 49.0161 | 15.3401 | -2.3666 | 2 | 4.9938 | 0.1102 | -1.2175 | 2.833 | 0.2497 | 3.6634 | 0.1715 | -0.1511 | 0.0566 | 0.02 | -0.0648 | -0.5159 | -0.0619 | 0.3719 | -0.0861 | 0.186 | -0.0351 | -0.0044 | 0.11 | 0.0339 | 0.2332 | 50.9392 | 24.2379 | 1.6997 | 3 | 2.197 | 1.1579 | 0.304 | 5.7399 | 0.8676 | 4.8791 | -0.0615 | 0.0968 | 0.236 | -0.1955 | 0.072 | 0.0158 | -0.1968 | -0.017 | 0.017 | 0.1225 | -0.0135 | -0.0007 | 0.1218 | 0.0307 | 0.1439 | 40.0317 | 25.0621 | -4.5666 | 4 | 1.8505 | -0.6374 | -1.7935 | 0.834 | -0.4457 | 3.9482 | 0.0891 | -0.208 | 0.0947 | 0.0399 | -0.0475 | 0.019 | -0.3611 | 0.0311 | -0.0671 | 0.1735 | -0.0332 | -0.0131 | 0.1143 | -0.0455 | 0.1585 | 33.7567 | 22.0458 | 19.5927 | 5 | 2.9437 | -0.3056 | -2.3664 | 3.8588 | 2.7357 | 7.2218 | 0.0283 | 0.1928 | 0.2212 | -0.2017 | -0.17 | 0.2388 | -0.4375 | -0.3006 | 0.1113 | 0.1319 | 0.0149 | -0.0019 | 0.0899 | 0.0337 | 0.1474 | 31.9447 | 21.1906 | -3.3902 | 6 | 1.0524 | -0.0308 | 0.8539 | 0.476 | -0.5733 | 1.6293 | 0.0157 | 0.01 | 0.019 | -0.0647 | 0.0193 | 0.0013 | -0.0579 | 0.1 | -0.0193 | 0.1254 | 0.0029 | 0.0182 | 0.09 | -0.0095 | 0.1159 | 32.5367 | 10.9256 | 7.5641 | 7 | 2.0707 | -0.039 | 2.728 | 2.5357 | -0.8004 | 6.3065 | 0.2651 | -0.0032 | -0.2434 | -0.1555 | 0.0817 | -0.0639 | 0.0827 | 0.2014 | -0.3341 | 0.0753 | 0.0055 | 0.0331 | 0.0837 | 0.0019 | 0.1116 | 40.3198 | 8.2237 | 6.0648 | 8 | 6.4619 | -0.1292 | -5.5932 | 5.4343 | 0.9078 | 9.3797 | 0.1028 | -0.2423 | 0.291 | -0.1984 | -0.0557 | -0.5495 | -0.4177 | -0.1256 | -0.0836 | 0.1646 | -0.0161 | -0.0505 | 0.2274 | -0.0509 | 0.2502 | 45.9563 | 16.1562 | 24.154 | 9 | 2.675 | 1.846 | 2.2594 | 4.2922 | 5.2613 | 6.4692 | 0.1069 | -0.4193 | 0.0062 | 0.6992 | -0.0139 | -0.3836 | 0.4011 | 0.0388 | -0.1192 | 0.1872 | -0.0307 | -0.0665 | 0.3292 | 0.0298 | 0.2125 | 46.8097 | 6.1963 | 29.1365 | 10 | 1.2301 | 0.6442 | -1.0618 | 2.1938 | -3.5035 | 8.6072 | 0.0283 | -0.1525 | 0.0621 | 0.0546 | -0.1495 | -0.2249 | -0.1926 | 0.3801 | 0.181 | 0.0981 | -0.0001 | 0.0093 | 0.0881 | 0.0028 | 0.1349 | 47.5104 | 3.6426 | 8.906 | 11 | 1.3311 | -0.4494 | -0.3342 | 1.5016 | 0.6379 | 0.2306 | 0.0849 | -0.0032 | -0.0408 | -0.1523 | 0.0079 | -0.037 | -0.0578 | 0.0566 | -0.0927 | 0.1059 | -0.0176 | 0.0252 | 0.0685 | 0.0075 | 0.1221 | 38.6222 | 1.8423 | 6.5095 | 12 | 1.3946 | -0.0625 | 0.1885 | 2.1432 | -0.4646 | 1.1476 | 0.0388 | -0.1677 | 0.13 | 0.0391 | -0.0338 | 0.4362 | -0.0019 | -0.1328 | -0.0259 | 0.1099 | 0.0268 | 0.0149 | 0.2758 | -0.088 | 0.232 | 4.3101 | 17.6686 | 26.515 | 13 | 1.1714 | -2.0623 | 1.1017 | 6.5394 | 1.0922 | 4.5619 | -0.2012 | -0.3137 | 0.3912 | 0.2561 | 0.2506 | -0.2119 | -0.4168 | 0.1016 | -0.0243 | 0.1393 | 0.0024 | 0.0081 | 0.2385 | -0.1071 | 0.214 | 13.8899 | 24.2043 | 30.3223 | 14 | 1.3953 | 0.2404 | -0.2221 | 1.7784 | -0.9905 | 4.333 | 0.0177 | -0.0059 | 0.242 | -0.0557 | -0.0266 | -0.04 | -0.1944 | -0.089 | -0.0244 | 0.1723 | 0.0308 | 0.0009 | 0.0802 | -0.0127 | 0.175 | 20.0213 | 22.0809 | 6.0296 | 15 | 0.8903 | -0.0873 | 0.2346 | 0.8764 | -0.2309 | 2.0474 | 0.0119 | -0.2267 | 0.1511 | 0.0513 | 0.0194 | 0.0299 | -0.1525 | -0.1361 | -0.0352 | 0.0898 | 0.012 | 0.0087 | 0.1424 | -0.0388 | 0.1291 | 21.4738 | 13.3458 | 21.3221 | 16 | 1.4862 | -0.2286 | 1.8428 | 2.106 | 0.1778 | 4.6919 | 0.0717 | -0.2385 | -0.0238 | -0.056 | -0.0248 | 0.1753 | -0.1496 | -0.4455 | -0.1557 | 0.0713 | 0.0128 | 0.0339 | 0.1943 | -0.0205 | 0.1189 | 13.8304 | 7.6716 | 18.9769 | 17 | 4.688 | -1.1766 | -4.8345 | 2.2264 | 1.4424 | 5.0019 | 0.1263 | 0.1489 | 0.6812 | -0.3015 | 0.0224 | 0.314 | -0.6777 | -0.1253 | -0.1869 | 0.2438 | 0.0421 | -0.0786 | 0.2345 | 0.0218 | 0.3421 | 7.7855 | 15.413 | 0.0972 | 18 | 4.2195 | -3.1878 | 3.9788 | 8.7834 | -6.5188 | 7.992 | 0.075 | 0.2441 | 0.1511 | -0.4293 | -0.0075 | 0.4889 | 0.182 | -0.2589 | -0.0697 | 0.2164 | 0.0174 | -0.0526 | 0.2761 | -0.0165 | 0.1864 | 7.4641 | 6.1533 | -3.7892 | 19 | 1.3771 | -0.0941 | 0.1636 | 1.2582 | 0.5217 | 2.3421 | -0.0087 | -0.1587 | 0.0593 | -0.0013 | -0.0462 | 0.0739 | -0.0485 | -0.1846 | 0.06 | 0.08 | -0.0006 | 0.0083 | 0.1339 | -0.0103 | 0.1175 | 10.9583 | 2.2534 | 17.3274 | 20 | 2.0623 | -0.1206 | 0.3827 | 3.182 | -0.8624 | 2.0919 | 0.1279 | -0.4191 | -0.0604 | 0.4549 | -0.2054 | 0.2064 | 0.1651 | -0.3782 | 0.0028 | 0.1977 | -0.0934 | 0.0345 | 0.3159 | 0.0503 | 0.1948 | 6.1435 | -16.8242 | 28.3365 | 21 | 0.7922 | 0.8742 | -0.1905 | 1.0933 | -0.9725 | 3.1046 | 0.2196 | -0.5472 | -0.3109 | 0.2786 | -0.242 | 0.0743 | 0.3861 | -0.1936 | 0.0696 | 0.2264 | -0.1023 | 0.0128 | 0.337 | 0.1186 | 0.2931 | 7.4761 | -25.7506 | 24.5469 | 22 | 4.3984 | -0.8345 | 0.6063 | 0.7998 | 0.3319 | 0.496 | 0.0381 | -0.159 | -0.4131 | -0.1306 | -0.0436 | -0.0032 | 0.138 | 0.0492 | 0.0089 | 0.1444 | -0.0099 | -0.0052 | 0.1466 | 0.0846 | 0.1716 | 31.3223 | -23.6221 | 20.8546 | 23 | 4.2234 | -2.6525 | -1.0388 | 4.1512 | 0.3194 | 2.3262 | 0.1199 | 0.1267 | -0.6042 | -0.1197 | -0.1272 | 0.3905 | 0.1641 | -0.2116 | -0.001 | 0.1302 | -0.0367 | 0.0278 | 0.141 | 0.0192 | 0.2003 | 10.4447 | -22.692 | 11.7924 | 24 | 1.1454 | 0.1241 | 0.1136 | 0.8205 | 0.0885 | 1.3083 | -0.0331 | -0.2319 | -0.1482 | 0.0007 | -0.0088 | 0.0076 | -0.0135 | -0.1456 | 0.0419 | 0.1021 | -0.0127 | 0.0089 | 0.1153 | 0.0272 | 0.1039 | 19.6327 | -11.5628 | 17.5279 | 25 | 4.9048 | 0.6958 | -4.5622 | 6.5287 | -1.4357 | 4.4798 | 0.0291 | -0.2781 | -0.618 | 0.269 | -0.0614 | 0.2455 | 0.2608 | 0.0782 | 0.062 | 0.2035 | -0.0172 | -0.0034 | 0.2793 | 0.0598 | 0.1664 | 33.2513 | -16.7961 | 34.0049 | 26 | 7.4824 | -4.7753 | 4.5635 | 7.3877 | -2.065 | 5.2836 | -0.1478 | -0.4542 | 0.4242 | 0.6664 | 0.0063 | -0.5084 | -0.0033 | -0.2192 | 0.1157 | 0.1543 | -0.0319 | -0.0642 | 0.3912 | 0.0178 | 0.1889 | 36.3763 | -7.6895 | 36.6233 | 27 | 4.5893 | 1.4768 | 2.1383 | 1.688 | 0.6414 | 2.9445 | 0.0683 | -0.5667 | -0.2298 | 0.177 | -0.1171 | -0.0386 | 0.0535 | -0.2489 | 0.0124 | 0.12 | -0.0005 | 0.0268 | 0.2492 | 0.0215 | 0.1219 | 17.3101 | -4.9315 | 30.5466 | 28 | 0.559 | -0.8168 | -0.7005 | 1.9229 | 0.1926 | 1.7358 | -0.0184 | -0.2074 | -0.1439 | -0.0097 | 0.0146 | 0.0109 | -0.11 | -0.1863 | -0.026 | 0.1049 | -0.0179 | 0.0296 | 0.1121 | 0.0246 | 0.0725 | 17.8796 | -3.0939 | 21.4172 | 29 | 2.8686 | 1.0167 | 0.4429 | 4.6023 | 0.299 | 3.1453 | -0.0015 | -0.0134 | 0.034 | -0.4602 | -0.0235 | -0.2742 | -0.0435 | 0.1558 | -0.0008 | 0.1508 | 0.0327 | 0.0645 | 0.112 | 0.0153 | 0.1421 | 48.7837 | -15.5354 | -3.6789 | 30 | 1.8024 | 1.126 | -1.1462 | 3.4796 | -3.6233 | 7.7269 | -0.0044 | 0.2522 | -0.0319 | -0.6919 | -0.0488 | -0.1795 | 0.0787 | -0.1422 | 0.0045 | 0.3926 | 0.0497 | 0.079 | 0.1408 | 0.0069 | 0.1805 | 45.997 | -24.4678 | -7 | 31 | 1.8696 | -0.0112 | 2.1543 | 6.0316 | 0.1398 | 2.6708 | -0.0291 | 0.0356 | -0.1961 | 0.333 | 0.1846 | -0.0873 | 0.3452 | 0.112 | -0.1312 | 0.1505 | 0.0247 | 0.0554 | 0.105 | -0.0019 | 0.1162 | 48.2898 | -25.5063 | 5.3335 | 32 | 1.3613 | -0.1307 | 0.3531 | 0.6981 | 0.0727 | 0.8619 | 0.0059 | 0.0072 | -0.1114 | -0.0383 | -0.034 | 0.0052 | 0.0317 | 0.063 | 0.0268 | 0.1245 | 0.004 | 0.0218 | 0.099 | 0.0154 | 0.1165 | 33.735 | -16.2567 | 7.4426 | 33 | 9.6164 | -1.6037 | -5.2057 | 1.2781 | -0.1184 | 3.817 | -0.1394 | 0.4802 | -0.5258 | -0.2301 | 0.0308 | 0.0139 | 0.207 | -0.2353 | 0.1321 | 0.4355 | -0.0557 | -0.0455 | 0.255 | -0.0492 | 0.2623 | 21.3914 | -16.7056 | -10.28 | 34 | 9.6756 | 5.0817 | 4.3715 | 9.7711 | 4.1998 | 6.416 | -0.1511 | 0.3003 | -0.161 | -0.6456 | -0.1384 | 0.2539 | 0.2745 | -0.4635 | 0.3152 | 0.3499 | 0.0104 | -0.0101 | 0.36 | 0.0001 | 0.2326 | 18.1384 | -7.7389 | -11.8888 | 35 | 2.3831 | -0.1923 | 0.2314 | 0.7465 | 0.0177 | 1.302 | 0.0133 | 0.1555 | -0.0205 | -0.1279 | -0.0457 | -0.0241 | 0.0231 | 0.0553 | 0.0191 | 0.1437 | 0.0029 | 0.0239 | 0.0784 | 0.0075 | 0.13 | 36.8078 | -3.4411 | -1.404 |
|
---|
Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 2 through 52 )A2 - 52 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 53 through 70 )A53 - 70 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 71 through 93 )A71 - 93 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 94 through 120 )A94 - 120 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 121 through 136 )A121 - 136 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 137 through 182 )A137 - 182 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 183 through 196 )A183 - 196 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 197 through 210 )A197 - 210 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 211 through 224 )A211 - 224 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 225 through 244 )A225 - 244 | 11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 245 through 265 )A245 - 265 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 4 through 70 )B4 - 70 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 71 through 93 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|