Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementHKL-2000 | | data reductionHKL-2000 | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4YCB chain A Resolution: 1.791→43.151 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.26 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1637 | 1880 | 4.76 % | Same as 4ZC8 |
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Rwork | 0.1379 | - | - | - |
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obs | 0.1391 | 39524 | 99.91 % | - |
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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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Refinement step | Cycle: LAST / Resolution: 1.791→43.151 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2335 | 0 | 17 | 354 | 2706 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 2516 | X-RAY DIFFRACTION | f_angle_d1.027 | 3464 | X-RAY DIFFRACTION | f_dihedral_angle_d12.193 | 933 | X-RAY DIFFRACTION | f_chiral_restr0.047 | 416 | X-RAY DIFFRACTION | f_plane_restr0.005 | 450 | | | | | |
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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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1.7913-1.8397 | 0.2172 | 137 | 0.1775 | 2847 | X-RAY DIFFRACTION | 99 | 1.8397-1.8938 | 0.19 | 149 | 0.151 | 2838 | X-RAY DIFFRACTION | 100 | 1.8938-1.955 | 0.1601 | 138 | 0.1434 | 2847 | X-RAY DIFFRACTION | 100 | 1.955-2.0248 | 0.1683 | 143 | 0.1413 | 2871 | X-RAY DIFFRACTION | 100 | 2.0248-2.1059 | 0.1624 | 144 | 0.138 | 2852 | X-RAY DIFFRACTION | 100 | 2.1059-2.2017 | 0.162 | 142 | 0.1372 | 2867 | X-RAY DIFFRACTION | 100 | 2.2017-2.3178 | 0.1624 | 144 | 0.1306 | 2886 | X-RAY DIFFRACTION | 100 | 2.3178-2.463 | 0.1748 | 141 | 0.1386 | 2869 | X-RAY DIFFRACTION | 100 | 2.463-2.6532 | 0.1744 | 147 | 0.1428 | 2888 | X-RAY DIFFRACTION | 100 | 2.6532-2.9201 | 0.1889 | 145 | 0.1524 | 2906 | X-RAY DIFFRACTION | 100 | 2.9201-3.3425 | 0.1544 | 146 | 0.1436 | 2920 | X-RAY DIFFRACTION | 100 | 3.3425-4.2107 | 0.1494 | 148 | 0.1272 | 2954 | X-RAY DIFFRACTION | 100 | 4.2107-43.1638 | 0.1489 | 156 | 0.1268 | 3099 | X-RAY DIFFRACTION | 100 |
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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 | 2.6291 | -2.1264 | 0.775 | 1.8247 | -1.2844 | 4.5077 | 0.1393 | -0.3974 | 0.4009 | 0.348 | -0.0354 | 0.0827 | -0.263 | 0.0234 | -0.0373 | 0.0986 | 0.0049 | 0.0139 | 0.1213 | -0.0772 | 0.1262 | -5.7377 | 30.2912 | 35.703 | 2 | 4.6574 | 4.335 | -1.2338 | 4.4518 | -1.4216 | 1.8864 | 0.0528 | -0.477 | -0.0039 | 0.1933 | -0.1369 | -0.0559 | 0.1356 | 0.0529 | 0.0671 | 0.1683 | 0.0068 | -0.0128 | 0.2139 | -0.027 | 0.1211 | -0.6668 | 22.9823 | 41.0836 | 3 | 6.4555 | 4.2455 | 1.5952 | 3.8152 | 1.1636 | 0.68 | 0.1264 | -0.3787 | 0.0838 | 0.2724 | -0.1428 | -0.1006 | 0.0399 | -0.0851 | 0.0167 | 0.1455 | -0.0049 | -0.0015 | 0.135 | -0.046 | 0.1082 | -8.0633 | 27.5913 | 36.1108 | 4 | 6.1652 | 5.27 | -4.2435 | 4.6804 | -3.6554 | 2.9424 | 0.0387 | 0.1506 | 0.6259 | 0.0166 | 0.0492 | 0.4102 | -0.1558 | -0.1147 | -0.1364 | 0.1294 | 0.0337 | -0.0035 | 0.11 | -0.0399 | 0.1613 | -16.2573 | 30.517 | 28.6693 | 5 | 2.5662 | -0.7954 | 0.3935 | 3.0863 | 0.268 | 2.6027 | 0.0208 | -0.0578 | 0.1719 | -0.0373 | -0.0921 | 0.0692 | -0.0895 | -0.1158 | 0.0504 | 0.0682 | -0.0026 | 0.0002 | 0.0911 | -0.0302 | 0.0912 | -7.3846 | 26.8918 | 27.0659 | 6 | 3.1349 | -1.0662 | -2.0423 | 1.5888 | 0.0199 | 1.7199 | 0.3518 | -1.125 | -0.6801 | 1.4249 | -0.3672 | -0.5044 | 0.298 | 0.1435 | 0.1578 | 0.3434 | -0.087 | -0.0425 | 0.2879 | 0.058 | 0.2055 | -4.46 | 5.8645 | 34.573 | 7 | 2.1222 | 1.5579 | 0.402 | 3.0267 | 0.2231 | 1.3687 | -0.0243 | -0.0301 | 0.0257 | 0.0348 | -0.0217 | 0.0037 | -0.03 | -0.0264 | 0.0504 | 0.0578 | 0.0167 | 0.001 | 0.0865 | -0.0184 | 0.0631 | 1.3237 | 22.3084 | 26.4831 | 8 | 3.3896 | -3.8453 | 2.5189 | 5.4455 | -2.4758 | 2.2344 | 0.0751 | 0.1266 | -0.0682 | -0.1218 | -0.1013 | 0.0884 | -0.0171 | 0.146 | 0.0291 | 0.141 | -0.0266 | -0.0297 | 0.1193 | -0.0474 | 0.1209 | 15.3755 | 32.0727 | 35.2264 | 9 | 8.2734 | -4.9603 | 2.2036 | 5.7765 | -5.8374 | 8.8936 | 0.0728 | -0.4068 | -0.3956 | 0.701 | 0.119 | -0.5406 | 0.4996 | 0.1402 | -0.1843 | 0.2746 | 0.0114 | -0.0937 | 0.1894 | -0.0351 | 0.1781 | 24.5452 | 14.2947 | 43.2706 | 10 | 5.5308 | -0.1082 | 0.5315 | 0.1776 | 0.9348 | 4.7801 | 0.138 | 0.1483 | 0.3294 | -0.4551 | -0.0821 | -0.0084 | -0.2266 | 0.0482 | 0.0195 | 0.1352 | -0.0256 | 0.0086 | 0.1233 | 0.0324 | 0.0836 | 13.7344 | 27.9643 | 11.5176 | 11 | 4.0945 | -2.9512 | -1.8686 | 6.8854 | 2.8088 | 3.5963 | 0.1036 | 0.3592 | 0.0205 | -0.2581 | -0.15 | 0.1499 | -0.0777 | -0.216 | 0.0443 | 0.1307 | -0.0127 | -0.0188 | 0.1712 | 0.0099 | 0.0582 | 6.9559 | 22.2548 | 6.015 | 12 | 2.2289 | -0.6653 | 0.0763 | 1.6218 | -0.3663 | 0.9744 | 0.0293 | 0.0484 | 0.1573 | -0.0375 | -0.0669 | -0.1061 | -0.0534 | 0.0915 | 0.0421 | 0.1227 | -0.0164 | -0.0152 | 0.0985 | 0.0098 | 0.0904 | 16.6484 | 24.4958 | 17.5606 | 13 | 6.1503 | 4.2829 | 0.0602 | 3.0238 | 0.3218 | 6.293 | 0.0475 | 0.9015 | -0.3478 | -1.3207 | -0.0129 | 0.4379 | 0.4764 | -0.0917 | 0.1029 | 0.2944 | 0.0458 | -0.0366 | 0.2519 | -0.0537 | 0.166 | 5.9442 | 4.6369 | 12.1414 | 14 | 1.3777 | -1.0097 | 0.1494 | 3.6616 | -0.3591 | 1.4853 | -0.0207 | -0.0031 | 0.0418 | -0.0073 | 0.0158 | 0.004 | -0.0376 | 0.0475 | 0.0114 | 0.0504 | -0.0156 | 0.0018 | 0.0937 | -0.0092 | 0.0582 | 4.6779 | 21.7494 | 20.5599 | 15 | 2.4973 | 2.1711 | 2.2799 | 2.0074 | 2.0117 | 2.1197 | -0.1548 | -0.04 | 0.4095 | -0.0086 | 0.1106 | 0.4086 | -0.2624 | -0.124 | 0.0837 | 0.2008 | 0.0148 | -0.0357 | 0.1451 | 0.0335 | 0.1967 | -6.5499 | 35.175 | 12.4262 | 16 | 2.4782 | 2.8808 | 1.1154 | 6.7174 | 3.8378 | 6.5775 | -0.3261 | 0.3344 | -0.0483 | -0.496 | 0.0378 | 0.7356 | 0.049 | -0.409 | 0.2094 | 0.2252 | -0.0361 | -0.0556 | 0.2324 | 0.0137 | 0.1612 | -21.3677 | 17.9348 | 2.1827 |
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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 20 through 30 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 31 through 46 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 47 through 61 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 62 through 72 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 73 through 107 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 108 through 114 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 115 through 154 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 155 through 171 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 172 through 179 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 20 through 30 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 31 through 46 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 47 through 107 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 108 through 114 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 115 through 154 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 155 through 171 )16 | X-RAY DIFFRACTION | 16 | chain 'B' | | | | | | | | | | | | | | | |
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