Software | Name | Version | Classification |
---|
PHENIX | 1.9_1692refinementXDS | | data reductionXSCALE | | data scalingSHARP | | phasing | | | | |
|
---|
Refinement | Method to determine structure: SAD / Resolution: 1.548→49.16 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 17.82
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.1834 | 3464 | 5 % |
---|
Rwork | 0.1536 | - | - |
---|
obs | 0.1551 | 136282 | 98.92 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
---|
Refinement step | Cycle: LAST / Resolution: 1.548→49.16 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 3569 | 0 | 64 | 506 | 4139 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.009 | 3785 | X-RAY DIFFRACTION | f_angle_d1.368 | 5200 | X-RAY DIFFRACTION | f_dihedral_angle_d13.424 | 1262 | X-RAY DIFFRACTION | f_chiral_restr0.058 | 589 | X-RAY DIFFRACTION | f_plane_restr0.005 | 650 | | | | | |
|
---|
LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
---|
1.5484-1.566 | 0.2695 | 170 | 0.254 | 3313 | X-RAY DIFFRACTION | 76 | 1.566-1.5845 | 0.235 | 229 | 0.234 | 4351 | X-RAY DIFFRACTION | 100 | 1.5845-1.6038 | 0.2899 | 232 | 0.2302 | 4385 | X-RAY DIFFRACTION | 100 | 1.6038-1.6241 | 0.2344 | 223 | 0.2209 | 4289 | X-RAY DIFFRACTION | 100 | 1.6241-1.6454 | 0.2651 | 232 | 0.2111 | 4409 | X-RAY DIFFRACTION | 99 | 1.6454-1.668 | 0.2253 | 229 | 0.2035 | 4316 | X-RAY DIFFRACTION | 100 | 1.668-1.6918 | 0.2232 | 233 | 0.1954 | 4420 | X-RAY DIFFRACTION | 100 | 1.6918-1.7171 | 0.2079 | 225 | 0.1923 | 4277 | X-RAY DIFFRACTION | 100 | 1.7171-1.7439 | 0.1988 | 228 | 0.1889 | 4344 | X-RAY DIFFRACTION | 100 | 1.7439-1.7725 | 0.2118 | 227 | 0.1828 | 4300 | X-RAY DIFFRACTION | 100 | 1.7725-1.8031 | 0.2134 | 233 | 0.1788 | 4417 | X-RAY DIFFRACTION | 100 | 1.8031-1.8359 | 0.1979 | 226 | 0.164 | 4342 | X-RAY DIFFRACTION | 100 | 1.8359-1.8712 | 0.1749 | 228 | 0.1613 | 4363 | X-RAY DIFFRACTION | 100 | 1.8712-1.9094 | 0.1711 | 229 | 0.1598 | 4344 | X-RAY DIFFRACTION | 100 | 1.9094-1.9509 | 0.1855 | 232 | 0.1583 | 4369 | X-RAY DIFFRACTION | 100 | 1.9509-1.9963 | 0.1841 | 227 | 0.1539 | 4327 | X-RAY DIFFRACTION | 100 | 1.9963-2.0462 | 0.209 | 232 | 0.1496 | 4398 | X-RAY DIFFRACTION | 100 | 2.0462-2.1015 | 0.1836 | 230 | 0.1507 | 4326 | X-RAY DIFFRACTION | 100 | 2.1015-2.1633 | 0.1928 | 227 | 0.1489 | 4319 | X-RAY DIFFRACTION | 100 | 2.1633-2.2332 | 0.1933 | 231 | 0.154 | 4398 | X-RAY DIFFRACTION | 100 | 2.2332-2.313 | 0.1999 | 229 | 0.1508 | 4339 | X-RAY DIFFRACTION | 100 | 2.313-2.4056 | 0.1934 | 230 | 0.1475 | 4384 | X-RAY DIFFRACTION | 100 | 2.4056-2.5151 | 0.181 | 229 | 0.1437 | 4350 | X-RAY DIFFRACTION | 100 | 2.5151-2.6477 | 0.195 | 228 | 0.1502 | 4335 | X-RAY DIFFRACTION | 100 | 2.6477-2.8135 | 0.2138 | 228 | 0.1503 | 4328 | X-RAY DIFFRACTION | 100 | 2.8135-3.0307 | 0.1842 | 225 | 0.1546 | 4349 | X-RAY DIFFRACTION | 99 | 3.0307-3.3357 | 0.1878 | 227 | 0.1503 | 4324 | X-RAY DIFFRACTION | 99 | 3.3357-3.8182 | 0.1574 | 231 | 0.1358 | 4353 | X-RAY DIFFRACTION | 99 | 3.8182-4.8099 | 0.1294 | 228 | 0.1167 | 4359 | X-RAY DIFFRACTION | 100 | 4.8099-49.1858 | 0.1558 | 236 | 0.1481 | 4340 | X-RAY DIFFRACTION | 100 |
|
---|
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 | 2.0496 | -0.4361 | 0.4152 | 2.1075 | -0.2217 | 1.8402 | -0.1265 | -0.2787 | 0.0107 | 0.4157 | 0.1159 | -0.1453 | -0.0166 | 0.1261 | 0.0232 | 0.2906 | 0.0736 | -0.0344 | 0.2077 | -0.0011 | 0.1213 | -0.9548 | 24.5883 | 77.2822 | 2 | 1.9058 | -0.4639 | 0.0187 | 1.9988 | -0.4111 | 2.0223 | -0.1788 | -0.1512 | -0.026 | 0.2905 | 0.1224 | -0.0874 | 0.0183 | 0.0671 | 0.0544 | 0.1648 | 0.0553 | -0.0162 | 0.1217 | 0.0016 | 0.0805 | -0.9529 | 21.536 | 70.4733 | 3 | 2.7121 | 1.7437 | 2.4397 | 2.9295 | 1.0999 | 4.2475 | -0.1027 | -0.0217 | 0.188 | 0.3042 | 0.142 | -0.1586 | -0.2743 | 0.2266 | 0.0402 | 0.1623 | 0.0237 | -0.0247 | 0.1034 | -0.0175 | 0.1478 | -1.0682 | 30.2662 | 68.2016 | 4 | 6.9955 | 2.2763 | 2.1964 | 2.9963 | 0.1136 | 2.8015 | -0.0564 | -0.0758 | 0.0232 | 0.2019 | 0.1587 | 0.148 | -0.073 | -0.1858 | -0.104 | 0.1232 | 0.0569 | 0.0238 | 0.1349 | 0.015 | 0.1022 | -12.0243 | 26.8829 | 65.2318 | 5 | 1.0682 | 0.0598 | -0.0418 | 2.0232 | -0.6651 | 1.5385 | -0.0425 | 0.0513 | 0.2446 | 0.2485 | 0.2052 | 0.1884 | -0.3347 | -0.2547 | -0.1516 | 0.1885 | 0.045 | 0.0275 | 0.1279 | 0.0549 | 0.1834 | -10.2574 | 47.9882 | 52.8313 | 6 | 2.5176 | -0.0578 | -0.8418 | 2.4662 | -0.3253 | 2.3591 | -0.0639 | 0.2136 | 0.2872 | -0.0534 | 0.1686 | 0.017 | -0.1544 | -0.0373 | -0.0797 | 0.1012 | -0.0155 | -0.0161 | 0.089 | 0.0364 | 0.1414 | -4.7548 | 42.3488 | 46.7929 | 7 | 3.1496 | -2.4129 | -1.6682 | 5.5758 | 1.885 | 3.7492 | 0.0288 | 0.0125 | 0.1009 | 0.0368 | 0.0993 | -0.002 | -0.0783 | -0.1111 | -0.0898 | 0.0776 | -0.0119 | 0.0027 | 0.0996 | 0.0206 | 0.0859 | -5.1028 | 34.6886 | 52.736 | 8 | 1.7051 | -1.1494 | -0.1124 | 6.3262 | 1.2109 | 3.0152 | -0.0224 | -0.0285 | 0.3843 | 0.2773 | 0.1094 | -0.251 | -0.5253 | 0.0902 | -0.105 | 0.2131 | 0.0018 | -0.0134 | 0.1051 | 0.0099 | 0.1883 | -3.5046 | 43.6796 | 58.9064 | 9 | 1.5353 | -0.1298 | 0.3301 | 2.7245 | -0.7855 | 3.2056 | -0.0804 | -0.0468 | -0.2782 | 0.0013 | 0.1378 | 0.1903 | 0.5961 | -0.0898 | -0.078 | 0.2429 | -0.0187 | 0.0406 | 0.1244 | -0.0254 | 0.2285 | -5.9636 | 7.0595 | 59.1441 | 10 | 1.578 | -0.6057 | -0.2036 | 1.6834 | -0.1352 | 1.6498 | -0.1384 | -0.099 | -0.246 | 0.0591 | 0.1215 | 0.1124 | 0.2567 | -0.0413 | 0.0367 | 0.1749 | 0.0086 | 0.0199 | 0.0998 | 0.006 | 0.1684 | -4.1175 | 11.819 | 62.6021 | 11 | 2.939 | -0.1992 | -0.0904 | 2.5116 | -0.1504 | 1.7536 | -0.1101 | 0.1138 | -0.0388 | -0.001 | 0.0733 | -0.1906 | 0.2472 | 0.1442 | 0.0397 | 0.1511 | 0.0229 | 0.0082 | 0.0979 | -0.0107 | 0.1155 | 2.9833 | 15.8552 | 58.9751 | 12 | 5.6174 | 2.2145 | -0.0152 | 5.4889 | -0.3087 | 2.7156 | -0.1631 | 0.1961 | -0.1445 | -0.2248 | 0.1279 | 0.3942 | 0.3886 | -0.344 | 0.0309 | 0.1511 | -0.0456 | -0.0084 | 0.1378 | -0.0223 | 0.1316 | -9.3483 | 16.108 | 56.3441 | 13 | 3.9167 | 2.4041 | -0.1044 | 5.3201 | -0.8498 | 0.9208 | -0.1328 | 0.0255 | 0.1559 | -0.1663 | 0.0406 | -0.0695 | -0.0557 | -0.0223 | 0.1136 | 0.1222 | 0.0088 | -0.001 | 0.1203 | -0.0191 | 0.1086 | 0.9663 | 27.9481 | 55.6504 | 14 | 7.1321 | -1.1637 | -4.3585 | 4.1236 | 0.9472 | 3.3501 | -0.4399 | 0.6889 | -0.5981 | -0.3467 | 0.0963 | -0.3243 | 0.4984 | 0.3751 | 0.2514 | 0.3932 | -0.0791 | 0.0791 | 0.2395 | -0.0899 | 0.3452 | -8.6828 | 3.9258 | 50.1845 | 15 | 0.355 | -0.3645 | 0.6786 | 1.1611 | -0.4244 | 1.3173 | -0.0811 | 0.3412 | 0.0763 | -0.328 | 0.2878 | 0.7021 | 0.0059 | -0.4021 | -0.1343 | 0.2056 | -0.1081 | -0.1696 | 0.3603 | 0.1821 | 0.2192 | -21.033 | 33.4962 | 40.2331 | 16 | 2.5873 | 0.104 | -0.0798 | 2.0392 | -0.6083 | 1.2778 | -0.018 | 0.267 | 0.0598 | -0.2775 | 0.2517 | 0.2952 | 0.0586 | -0.2977 | -0.09 | 0.138 | -0.0464 | -0.0505 | 0.2456 | 0.0928 | 0.1589 | -16.4019 | 35.5104 | 43.3571 | 17 | 2.0906 | 0.1063 | -0.0209 | 1.5503 | -1.0713 | 1.845 | -0.1051 | 0.1187 | 0.025 | 0.0098 | 0.2857 | 0.3665 | -0.0697 | -0.4529 | 0.0077 | 0.1014 | 0.0097 | -0.0116 | 0.1939 | 0.0936 | 0.1866 | -18.3447 | 33.8352 | 53.3138 | 18 | 1.7833 | -0.7553 | 1.111 | 1.8022 | 0.9304 | 6.5149 | -0.0396 | 0.3038 | -0.1487 | -0.243 | 0.1695 | 0.5122 | 0.3347 | -0.2495 | -0.0298 | 0.1859 | -0.1118 | -0.0739 | 0.2306 | 0.0654 | 0.2037 | -18.215 | 25.6137 | 46.7587 |
|
---|
Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
---|
1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 7 through 45 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 46 through 89 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 90 through 104 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 105 through 125 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 8 through 70 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 71 through 89 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 90 through 114 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 115 through 126 )9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 8 through 29 )10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 30 through 70 )11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 71 through 89 )12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 90 through 104 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 105 through 122 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 123 through 127 )15 | X-RAY DIFFRACTION | 15 | chain 'D' and (resid 9 through 36 )16 | X-RAY DIFFRACTION | 16 | chain 'D' | | | | | | | | | | | | | | | |
|
---|