Software | Name | Version | Classification |
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PHENIX | (1.11rc3_2553: ???)refinementXSCALE | | data scalingPDB_EXTRACT | 3.2 | data extractionXDS | | data reductionMoRDa | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EK2 Resolution: 1.85→38.181 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1763 | 2106 | 2.37 % |
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Rwork | 0.145 | - | - |
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obs | 0.1457 | 88760 | 99.9 % |
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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: 1.85→38.181 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 7482 | 0 | 212 | 942 | 8636 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 7909 | X-RAY DIFFRACTION | f_angle_d0.778 | 10754 | X-RAY DIFFRACTION | f_dihedral_angle_d8.884 | 4731 | X-RAY DIFFRACTION | f_chiral_restr0.051 | 1248 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1462 | | | | | |
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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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1.85-1.893 | 0.2629 | 135 | 0.1917 | 5697 | X-RAY DIFFRACTION | 100 | 1.893-1.9403 | 0.2351 | 138 | 0.1852 | 5733 | X-RAY DIFFRACTION | 100 | 1.9403-1.9928 | 0.2205 | 144 | 0.1804 | 5710 | X-RAY DIFFRACTION | 100 | 1.9928-2.0514 | 0.2025 | 149 | 0.1652 | 5721 | X-RAY DIFFRACTION | 100 | 2.0514-2.1176 | 0.2063 | 156 | 0.1592 | 5686 | X-RAY DIFFRACTION | 100 | 2.1176-2.1933 | 0.1926 | 143 | 0.1509 | 5718 | X-RAY DIFFRACTION | 100 | 2.1933-2.2811 | 0.1714 | 136 | 0.1501 | 5739 | X-RAY DIFFRACTION | 100 | 2.2811-2.3849 | 0.206 | 118 | 0.1531 | 5768 | X-RAY DIFFRACTION | 100 | 2.3849-2.5106 | 0.1819 | 131 | 0.1558 | 5750 | X-RAY DIFFRACTION | 100 | 2.5106-2.6679 | 0.1867 | 171 | 0.1458 | 5742 | X-RAY DIFFRACTION | 100 | 2.6679-2.8738 | 0.1814 | 136 | 0.1461 | 5777 | X-RAY DIFFRACTION | 100 | 2.8738-3.1629 | 0.1672 | 127 | 0.1433 | 5818 | X-RAY DIFFRACTION | 100 | 3.1629-3.6203 | 0.18 | 143 | 0.1308 | 5816 | X-RAY DIFFRACTION | 100 | 3.6203-4.56 | 0.1315 | 131 | 0.1182 | 5893 | X-RAY DIFFRACTION | 100 | 4.56-38.1891 | 0.145 | 148 | 0.1395 | 6086 | 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 | 3.4019 | 1.9077 | 0.4043 | 1.625 | -0.6337 | 4.4097 | 0.0621 | 0.019 | -0.1801 | 0.121 | 0.1602 | 0.2345 | 0.4677 | -0.1681 | -0.1856 | 0.1915 | -0.0071 | -0.0355 | 0.0895 | 0.0476 | 0.2008 | -13.6557 | -48.8814 | -13.0343 | 2 | 2.0102 | 0.3129 | -0.1974 | 6.1652 | 3.2173 | 3.5324 | 0.1134 | -0.2819 | -0.1783 | 0.4258 | 0.015 | 0.3537 | 0.4029 | -0.249 | -0.0961 | 0.1963 | -0.0069 | -0.0211 | 0.1798 | 0.0982 | 0.205 | -13.0097 | -49.5469 | -2.3168 | 3 | 2.6221 | -0.1485 | 1.2445 | 0.515 | 0.7654 | 2.4254 | 0.0358 | -0.0826 | -0.0646 | 0.1271 | -0.0184 | -0.0532 | 0.185 | 0.0358 | -0.0087 | 0.1894 | 0.0244 | -0.0005 | 0.1439 | 0.0447 | 0.0963 | -2.7638 | -42.7282 | -1.1169 | 4 | 1.8486 | -2.5959 | -0.4018 | 4.559 | 0.5262 | 0.2818 | -0.0577 | -0.0794 | -0.1531 | 0.2005 | 0.0889 | 0.2338 | 0.0555 | -0.0249 | -0.0303 | 0.1478 | 0.0202 | 0.0093 | 0.1444 | 0.0154 | 0.0869 | -14.5511 | -30.9171 | -6.0458 | 5 | 1.0576 | -0.6405 | 0.1295 | 1.03 | 0.0026 | 0.8494 | 0.0178 | -0.0237 | -0.1042 | 0.0398 | 0.0175 | 0.0494 | 0.0375 | 0.0371 | -0.0311 | 0.106 | -0.0079 | -0.0029 | 0.1054 | 0.0164 | 0.0958 | -9.8233 | -29.4437 | -12.4642 | 6 | 0.2729 | 0.3197 | 0.6657 | 1.7148 | 0.071 | 1.9839 | -0.286 | -0.4688 | -0.4294 | 0.3801 | 0.1587 | 0.3773 | 0.2307 | -0.1882 | 0.129 | 0.206 | 0.018 | 0.0698 | 0.1393 | 0.0668 | 0.1798 | -17.3452 | -37.2225 | -15.5764 | 7 | 5.3671 | -2.4444 | -4.391 | 1.4551 | 1.2399 | 7.0783 | -0.1691 | -0.4251 | -0.0162 | 0.3103 | -0.2163 | 0.065 | 0.4166 | -0.3207 | 0.3684 | 0.2067 | -0.0524 | 0.0033 | 0.2703 | 0.0301 | 0.3299 | -34.5084 | -31.5263 | -16.0879 | 8 | 3.1836 | -1.3515 | 0.283 | 2.0712 | -0.3954 | 1.4438 | -0.0431 | -0.0764 | -0.3012 | 0.1081 | 0.1186 | 0.268 | 0.1353 | -0.1201 | -0.0698 | 0.1377 | -0.0248 | -0.0116 | 0.0943 | 0.0102 | 0.1169 | -20.2596 | -38.0368 | -23.867 | 9 | 2.0001 | 0.5687 | 2 | 2.0001 | 1.9999 | 2.0001 | 6.2553 | -11.0966 | 13.5792 | -0.7947 | 1.0658 | -2.1809 | -18.2261 | 7.9562 | -7.3052 | 0.9719 | 0.0129 | 0.1884 | 0.7674 | -0.2802 | 0.8735 | -40.2794 | -25.1436 | -28.7902 | 10 | 2.3828 | 0.6183 | -0.3083 | 2.7275 | 0.5149 | 3.4679 | -0.0563 | -0.1534 | 0.2011 | 0.19 | -0.0568 | -0.2028 | -0.5117 | 0.3839 | 0.109 | 0.2861 | -0.0767 | -0.0424 | 0.146 | 0.0129 | 0.1556 | -6.8036 | 6.3898 | -14.3152 | 11 | 0.6027 | -0.2905 | 0.2451 | 1.1596 | -0.0606 | 0.9635 | -0.0335 | -0.0668 | 0.0652 | 0.1109 | 0.0263 | -0.1027 | -0.1702 | 0.0628 | -0.0048 | 0.1443 | -0.0172 | -0.0059 | 0.1172 | 0.0031 | 0.0903 | -10.1735 | -9.4216 | -10.2729 | 12 | 1.5826 | -0.122 | -1.0266 | 1.571 | 0.4761 | 2.4682 | -0.0903 | -0.0182 | 0.0543 | -0.0028 | 0.0746 | -0.2114 | -0.0419 | 0.2744 | 0.007 | 0.1237 | -0.0128 | -0.0202 | 0.1384 | 0.0333 | 0.1059 | -7.7921 | -8.1643 | -27.7885 | 13 | 2 | 2 | 2.0001 | 2 | 2 | 2 | -0.8608 | 10.4686 | 2.4181 | -3.3054 | 4.7819 | 3.9382 | 1.6421 | -12.7907 | -3.916 | 0.706 | -0.1982 | 0.2341 | 0.8002 | 0.3035 | 0.6473 | 4.0514 | -20.7877 | -43.1116 | 14 | 1.4854 | -0.329 | 1.2143 | 2.2165 | 0.0279 | 1.8176 | 0.2567 | 0.3537 | -0.3531 | -0.1626 | 0.0007 | -0.0978 | 0.4519 | 0.2733 | -0.2129 | 0.2784 | 0.0405 | -0.0409 | 0.2295 | -0.1229 | 0.294 | -17.822 | -50.0912 | -47.6616 | 15 | 1.0425 | 0.4221 | 0.0372 | 1.6465 | -0.1789 | 1.181 | 0.0256 | 0.1069 | -0.1686 | -0.1082 | -0.0131 | -0.0754 | 0.0673 | 0.0128 | -0.0039 | 0.1121 | 0.011 | -0.0186 | 0.1122 | -0.0306 | 0.1199 | -19.2972 | -32.5495 | -44.9867 | 16 | 2.5233 | 0.4685 | 0.6691 | 2.2348 | 0.2037 | 1.4994 | -0.0008 | 0.276 | -0.0659 | -0.2097 | 0.0379 | -0.1774 | 0.134 | 0.2517 | -0.0265 | 0.1588 | 0.0255 | -0.0025 | 0.1442 | -0.0045 | 0.0987 | -7.8784 | -36.5454 | -34.1608 | 17 | 4.317 | 0.1082 | 0.8951 | 4.9244 | 1.3904 | 5.4969 | -0.1064 | -0.1108 | 0.1176 | -0.0077 | -0.0594 | 0.2023 | -0.3911 | -0.1086 | 0.1112 | 0.1824 | 0.0146 | -0.0268 | 0.0787 | 0.0279 | 0.0957 | -25.239 | 3.2231 | -41.2985 | 18 | 1.4423 | -1.3551 | -0.1951 | 4.8451 | 1.0571 | 2.7369 | 0.0887 | 0.1799 | -0.0049 | -0.3625 | -0.2085 | 0.535 | -0.3707 | -0.3305 | 0.1245 | 0.1936 | 0.0132 | -0.0259 | 0.1886 | 0.0212 | 0.1625 | -28.9987 | 2.3723 | -51.9985 | 19 | 0.4645 | 0.2175 | 0.0119 | 1.7467 | -0.6158 | 0.9164 | 0.003 | 0.11 | 0.0103 | -0.106 | 0.0228 | 0.1274 | -0.0286 | -0.0298 | -0.0281 | 0.1136 | -0.0014 | -0.0046 | 0.1298 | -0.0046 | 0.0881 | -21.8808 | -13.7757 | -46.8922 | 20 | 3.7139 | 0.4351 | -0.8567 | 2.749 | -0.3061 | 2.1062 | -0.3257 | 0.4516 | 0.3887 | -0.142 | 0.3516 | 0.46 | 0.2245 | -0.3776 | -0.0186 | 0.1556 | -0.0365 | -0.0381 | 0.1463 | 0.0437 | 0.119 | -24.2867 | -9.731 | -37.243 | 21 | 4.946 | 1.7117 | 0.3704 | 5.5076 | -3.2786 | 3.9316 | 0.1024 | 0.0255 | -0.0365 | 0.0961 | 0.1059 | 0.411 | -0.1293 | -0.4549 | -0.1953 | 0.1096 | 0.0377 | 0.0253 | 0.153 | -0.0107 | 0.1683 | -35.1139 | -12.0751 | -24.476 | 22 | 2.4094 | 0.3801 | -0.4052 | 2.1099 | -0.0945 | 1.7209 | 0.0155 | -0.0321 | 0.0876 | -0.0227 | -0.0477 | 0.0996 | -0.2103 | 0.0027 | 0.0264 | 0.1126 | -0.0009 | -0.023 | 0.0959 | -0.013 | 0.0581 | -21.6146 | -7.5068 | -30.3543 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 1 through 30 )A1 - 30 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 31 through 55 )A31 - 55 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 56 through 80 )A56 - 80 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 81 through 109 )A81 - 109 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 110 through 178 )A110 - 178 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 179 through 200 )A179 - 200 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 201 through 213 )A201 - 213 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 214 through 258 )A214 - 258 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 259 through 259 )A259 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 1 through 54 )B1 - 54 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 55 through 178 )B55 - 178 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 179 through 258 )B179 - 258 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 259 through 259 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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