Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE)refinementXDS | | data reductionSCALA | | data scalingPHENIX | | phasing | | | | |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.65→53.234 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1825 | 3736 | 5 % |
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Rwork | 0.1491 | - | - |
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obs | 0.1508 | 74240 | 99.97 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 23.8 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.65→53.234 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10417 | 0 | 102 | 823 | 11342 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 10940 | X-RAY DIFFRACTION | f_angle_d1.049 | 14998 | X-RAY DIFFRACTION | f_dihedral_angle_d15.196 | 3922 | X-RAY DIFFRACTION | f_chiral_restr0.076 | 1721 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1982 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.6501-2.6836 | 0.2492 | 147 | 0.204 | 2640 | X-RAY DIFFRACTION | 100 | 2.6836-2.7189 | 0.2365 | 142 | 0.184 | 2553 | X-RAY DIFFRACTION | 100 | 2.7189-2.7562 | 0.2229 | 135 | 0.1819 | 2641 | X-RAY DIFFRACTION | 100 | 2.7562-2.7956 | 0.2424 | 132 | 0.1766 | 2601 | X-RAY DIFFRACTION | 100 | 2.7956-2.8373 | 0.2292 | 121 | 0.1791 | 2635 | X-RAY DIFFRACTION | 100 | 2.8373-2.8816 | 0.2315 | 143 | 0.1763 | 2566 | X-RAY DIFFRACTION | 100 | 2.8816-2.9289 | 0.2001 | 159 | 0.1726 | 2591 | X-RAY DIFFRACTION | 100 | 2.9289-2.9794 | 0.2293 | 140 | 0.178 | 2581 | X-RAY DIFFRACTION | 100 | 2.9794-3.0335 | 0.2371 | 134 | 0.1702 | 2608 | X-RAY DIFFRACTION | 100 | 3.0335-3.0919 | 0.1892 | 148 | 0.1738 | 2628 | X-RAY DIFFRACTION | 100 | 3.0919-3.155 | 0.217 | 138 | 0.1591 | 2569 | X-RAY DIFFRACTION | 100 | 3.155-3.2236 | 0.2002 | 130 | 0.1598 | 2623 | X-RAY DIFFRACTION | 100 | 3.2236-3.2985 | 0.1859 | 130 | 0.1568 | 2619 | X-RAY DIFFRACTION | 100 | 3.2985-3.381 | 0.1944 | 124 | 0.1592 | 2622 | X-RAY DIFFRACTION | 100 | 3.381-3.4724 | 0.1701 | 146 | 0.1474 | 2583 | X-RAY DIFFRACTION | 100 | 3.4724-3.5746 | 0.1647 | 135 | 0.1331 | 2635 | X-RAY DIFFRACTION | 100 | 3.5746-3.6899 | 0.1602 | 150 | 0.1263 | 2584 | X-RAY DIFFRACTION | 100 | 3.6899-3.8218 | 0.1733 | 130 | 0.1228 | 2615 | X-RAY DIFFRACTION | 100 | 3.8218-3.9748 | 0.1404 | 161 | 0.1249 | 2595 | X-RAY DIFFRACTION | 100 | 3.9748-4.1556 | 0.1541 | 116 | 0.1176 | 2636 | X-RAY DIFFRACTION | 100 | 4.1556-4.3746 | 0.1474 | 143 | 0.1122 | 2593 | X-RAY DIFFRACTION | 100 | 4.3746-4.6485 | 0.1333 | 143 | 0.1138 | 2616 | X-RAY DIFFRACTION | 100 | 4.6485-5.0072 | 0.1422 | 140 | 0.1173 | 2621 | X-RAY DIFFRACTION | 100 | 5.0072-5.5106 | 0.1656 | 130 | 0.1318 | 2627 | X-RAY DIFFRACTION | 100 | 5.5106-6.3069 | 0.1841 | 139 | 0.1556 | 2624 | X-RAY DIFFRACTION | 100 | 6.3069-7.9418 | 0.1965 | 139 | 0.163 | 2646 | X-RAY DIFFRACTION | 100 | 7.9418-53.2445 | 0.1952 | 141 | 0.1937 | 2652 | X-RAY DIFFRACTION | 99 |
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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) |
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1 | 0.6956 | -0.1162 | 0.4915 | 0.6858 | 0.145 | 1.2116 | 0.0059 | -0.0749 | -0.3038 | 0.029 | -0.0954 | -0.2201 | 0.0884 | 0.0507 | -0.2584 | 0.161 | 0.004 | -0.0803 | 0.1774 | 0.0621 | 0.082 | 55.5471 | 148.8467 | -73.2783 | 2 | 0.2682 | 0.0847 | 0.379 | 1.1374 | -0.1556 | 0.7229 | 0.0532 | -0.2336 | 0.0436 | -0.0537 | -0.1806 | 0.4506 | 0.1374 | -0.4134 | -0.2109 | 0.0586 | 0.1243 | -0.0645 | -0.0851 | 0.0219 | 0.2104 | 34.6786 | 160.6799 | -69.9938 | 3 | 0.5262 | -0.2223 | 0.3139 | 1.2483 | 0.1276 | 0.4479 | -0.0469 | -0.0937 | -0.0022 | 0.0384 | 0.065 | -0.0684 | -0.0857 | 0.2122 | 0.018 | 0.0534 | 0.0005 | -0.0258 | 0.0872 | 0.001 | 0.1091 | 49.7669 | 165.5928 | -71.2105 | 4 | 0.6171 | -0.7401 | -0.1364 | 1.1382 | -0.3668 | 0.8598 | -0.0527 | -0.1043 | 0.0439 | 0.2414 | 0.0388 | -0.2151 | -0.0881 | 0.1274 | 0.0144 | 0.0958 | 0.0094 | -0.0703 | 0.1422 | -0.0032 | 0.1325 | 52.9816 | 161.7585 | -67.2024 | 5 | 0.9104 | -0.04 | 0.3246 | 1.6073 | 0.8423 | 1.2303 | 0.1128 | 0.1529 | -0.1814 | -0.115 | 0.1787 | -0.1578 | 0.1892 | 0.3258 | 0.1646 | 0.19 | 0.1029 | -0.016 | 0.1553 | 0.0588 | 0.1601 | 48.9088 | 118.1897 | -59.1068 | 6 | 0.9359 | -0.2233 | 0.0077 | 0.4053 | 0.117 | 0.8176 | 0.1123 | 0.2807 | 0.4359 | -0.1288 | 0.2825 | -0.1955 | -0.0998 | -0.0255 | 0.2497 | 0.0544 | 0.0305 | -0.0195 | 0.0745 | 0.0164 | 0.1018 | 36.1037 | 137.2183 | -70.8536 | 7 | 1.3377 | -0.1976 | -0.4463 | 0.6689 | -0.1336 | 0.557 | -0.0209 | 0.2879 | 0.0376 | -0.2869 | 0.0114 | 0.0699 | -0.0152 | -0.1057 | 0.0384 | 0.0862 | 0.0202 | -0.052 | 0.1415 | -0.0034 | 0.0771 | 31.6031 | 128.9655 | -77.252 | 8 | 0.9676 | -0.0617 | 0.5214 | 0.4274 | -0.2858 | 0.3579 | 0.015 | -0.0959 | -0.1364 | -0.0093 | -0.0404 | -0.0321 | 0.2189 | -0.1391 | -0.0604 | 0.0772 | 0.0467 | -0.027 | 0.1268 | 0.0366 | 0.0871 | 28.959 | 124.2494 | -63.9231 | 9 | 2.5759 | -0.9743 | -0.0175 | 1.1581 | -0.2775 | 0.9694 | -0.0484 | -0.1883 | -0.1974 | -0.0288 | 0.0587 | 0.1081 | 0.2771 | -0.2289 | 0.0053 | 0.1056 | -0.0207 | -0.0174 | 0.1278 | 0.0075 | 0.0931 | 24.6525 | 120.6714 | -60.5197 | 10 | 1.0074 | 0.1736 | 0.1899 | 0.5933 | -0.0763 | 0.8148 | -0.0709 | 0.0272 | -0.236 | 0.0545 | 0.1488 | -0.0527 | 0.1358 | 0.0425 | -0.0245 | 0.1633 | 0.0741 | -0.0307 | 0.0886 | 0.0242 | 0.1322 | 39.2366 | 118.1973 | -65.1044 | 11 | 0.5059 | -0.0268 | 0.8212 | 0.6564 | 0.2237 | 3.2014 | -0.1815 | 0.0675 | 0.0483 | 0.0512 | -0.0441 | -0.3018 | -0.3943 | 0.6262 | -0.7593 | 0.0665 | 0.072 | 0.0944 | 0.1588 | -0.0434 | 0.0698 | 49.2869 | 130.7338 | -119.513 | 12 | 0.402 | 0.1798 | -0.3504 | 0.437 | -0.0811 | 0.2916 | 0.0428 | -0.2886 | 0.1408 | 0.1618 | -0.2226 | 0.1199 | -0.2092 | 0.0406 | -0.1439 | 0.1232 | 0.0406 | 0.032 | 0.2297 | -0.0893 | 0.0788 | 29.7801 | 141.5297 | -106.897 | 13 | 0.9221 | 0.329 | -0.2265 | 0.6283 | 0.4232 | 0.8297 | -0.0976 | -0.0734 | 0.3541 | -0.3289 | -0.038 | 0.2576 | -0.4783 | -0.2782 | -0.3633 | -0.0864 | 0.1442 | 0.0359 | 0.1073 | -0.0735 | 0.0983 | 23.8683 | 140.9271 | -117.3302 | 14 | 1.2048 | 0.2121 | -0.2126 | 0.4855 | 0.4051 | 0.3972 | -0.0303 | 0.1677 | -0.0248 | -0.0254 | 0.0035 | 0.1497 | 0.0481 | -0.1092 | 0.0135 | 0.0778 | 0.0566 | 0.0115 | 0.1253 | -0.003 | 0.0812 | 24.4169 | 128.5684 | -119.7114 | 15 | 3.2137 | -0.4076 | 0.104 | 0.4084 | 0.1132 | 0.0925 | 0.0542 | 0.0426 | -0.2727 | 0.2401 | -0.0042 | -0.0083 | 0.313 | 0.0744 | -0.0205 | 0.121 | 0.0843 | -0.0259 | 0.2172 | -0.0134 | 0.0979 | 38.6392 | 123.8165 | -103.3766 | 16 | 1.6342 | 0.022 | -0.7168 | 0.5862 | -0.3489 | 0.7666 | -0.0021 | 0.004 | -0.2343 | -0.1184 | 0.0844 | 0.0905 | 0.112 | -0.0423 | 0.0281 | 0.1075 | 0.0338 | 0.0114 | 0.1252 | -0.0718 | 0.0991 | 26.5657 | 121.1919 | -116.7485 | 17 | 0.8591 | 0.1399 | 0.0595 | 0.6631 | 0.0939 | 0.4459 | -0.0563 | 0.0973 | 0.0126 | -0.052 | 0.0693 | -0.0185 | -0.0244 | 0.0718 | 0.0038 | 0.0672 | 0.0496 | 0.0083 | 0.1343 | -0.037 | 0.0921 | 37.6259 | 130.0417 | -121.5712 | 18 | 1.01 | 0.1302 | 0.1128 | 0.1559 | -0.3064 | 1.0843 | 0.0196 | 0.032 | -0.178 | -0.3539 | -0.0187 | -0.4745 | 0.5227 | 0.48 | 0.164 | 0.2354 | 0.0831 | 0.2435 | 0.2323 | -0.087 | 0.5123 | 68.2571 | 152.6791 | -127.9183 | 19 | 0.885 | 0.0185 | 0.0186 | 0.8513 | 0.0501 | 0.2888 | 0.0683 | 0.0369 | -0.1637 | -0.0411 | 0.0476 | 0.0032 | 0.0551 | -0.0103 | -0.0053 | 0.153 | 0.0154 | 0.028 | 0.1277 | -0.0314 | 0.0867 | 45.4305 | 153.6272 | -116.0854 | 20 | 1.2459 | -0.3235 | 0.4047 | 0.9826 | -0.583 | 1.0293 | -0.0298 | -0.062 | 0.0253 | 0.1539 | 0.0241 | -0.085 | -0.0246 | 0.0327 | -0.0248 | 0.1131 | 0.0007 | -0.0067 | 0.0752 | -0.0296 | 0.0954 | 50.1207 | 161.6781 | -109.5339 | 21 | 0.9152 | -0.0233 | -0.2576 | 1.2111 | -0.3843 | 0.7593 | 0.0077 | 0.1879 | 0.2228 | -0.4211 | 0.0526 | -0.4372 | 0.1614 | 0.185 | -0.0264 | 0.2314 | 0.0109 | 0.1165 | 0.1041 | 0.0122 | 0.0465 | 52.7042 | 166.5174 | -123.0763 | 22 | 2.2507 | -0.5646 | 0.0276 | 0.8486 | -0.0813 | 0.9743 | -0.0392 | 0.1098 | 0.2837 | -0.4337 | 0.0038 | -0.3248 | -0.3196 | 0.1944 | -0.0261 | 0.2299 | -0.0584 | 0.0835 | 0.1202 | -0.0041 | 0.2034 | 53.5901 | 172.0645 | -126.1639 | 23 | 0.3851 | 0.1393 | -0.1984 | 0.4772 | 0.0315 | 0.5134 | 0.0236 | 0.1453 | 0.0618 | -0.2658 | 0.034 | -0.6533 | 0.0802 | 0.2839 | 0.009 | 0.1335 | -0.0017 | 0.2155 | 0.2101 | -0.0023 | 0.3253 | 63.3174 | 160.8516 | -121.6891 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | CHAIN A AND (RESID -1 THROUGH 58 ) | 2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESID 59 THROUGH 146 )3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESID 147 THROUGH 249 )4 | X-RAY DIFFRACTION | 4 | CHAIN A AND (RESID 250 THROUGH 337 )5 | X-RAY DIFFRACTION | 5 | CHAIN B AND (RESID 0 THROUGH 42 )6 | X-RAY DIFFRACTION | 6 | CHAIN B AND (RESID 43 THROUGH 80 )7 | X-RAY DIFFRACTION | 7 | CHAIN B AND (RESID 81 THROUGH 146 )8 | X-RAY DIFFRACTION | 8 | CHAIN B AND (RESID 147 THROUGH 249 )9 | X-RAY DIFFRACTION | 9 | CHAIN B AND (RESID 250 THROUGH 285 )10 | X-RAY DIFFRACTION | 10 | CHAIN B AND (RESID 286 THROUGH 337 )11 | X-RAY DIFFRACTION | 11 | CHAIN C AND (RESID -1 THROUGH 42 ) | 12 | X-RAY DIFFRACTION | 12 | CHAIN C AND (RESID 43 THROUGH 80 )13 | X-RAY DIFFRACTION | 13 | CHAIN C AND (RESID 81 THROUGH 146 )14 | X-RAY DIFFRACTION | 14 | CHAIN C AND (RESID 147 THROUGH 224 )15 | X-RAY DIFFRACTION | 15 | CHAIN C AND (RESID 225 THROUGH 249 )16 | X-RAY DIFFRACTION | 16 | CHAIN C AND (RESID 250 THROUGH 285 )17 | X-RAY DIFFRACTION | 17 | CHAIN C AND (RESID 286 THROUGH 337 )18 | X-RAY DIFFRACTION | 18 | CHAIN D | | | | | | | | | | | | | | | |
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