Software | Name | Classification |
---|
XDS | data reductionXSCALE | data scalingPHASER | phasingPHENIX | refinementCoot | model buildingPDB_EXTRACT | data extraction | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2i8b Resolution: 1.75→24.579 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.61 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.2078 | 2363 | 5.02 % | Random selection |
---|
Rwork | 0.1665 | 44746 | - | - |
---|
obs | 0.1686 | 47109 | 95.69 % | - |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
---|
Displacement parameters | Biso max: 71.47 Å2 / Biso mean: 21.9758 Å2 / Biso min: 5.87 Å2 |
---|
Refinement step | Cycle: final / Resolution: 1.75→24.579 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 3939 | 0 | 8 | 394 | 4341 |
---|
Biso mean | - | - | 47.17 | 31.7 | - |
---|
Num. residues | - | - | - | - | 516 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.01 | 4172 | X-RAY DIFFRACTION | f_angle_d1.095 | 5698 | X-RAY DIFFRACTION | f_chiral_restr0.063 | 700 | X-RAY DIFFRACTION | f_plane_restr0.006 | 709 | X-RAY DIFFRACTION | f_dihedral_angle_d16.448 | 2586 | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
---|
1.7501-1.7858 | 0.2804 | 149 | 0.2374 | 2686 | 2835 | 96 | 1.7858-1.8246 | 0.2715 | 130 | 0.2231 | 2634 | 2764 | 96 | 1.8246-1.867 | 0.2908 | 123 | 0.2161 | 2631 | 2754 | 96 | 1.867-1.9137 | 0.2738 | 118 | 0.2063 | 2650 | 2768 | 96 | 1.9137-1.9654 | 0.2818 | 129 | 0.1915 | 2669 | 2798 | 96 | 1.9654-2.0232 | 0.2169 | 166 | 0.1774 | 2650 | 2816 | 96 | 2.0232-2.0885 | 0.2033 | 156 | 0.1715 | 2603 | 2759 | 96 | 2.0885-2.1631 | 0.1936 | 152 | 0.1682 | 2650 | 2802 | 96 | 2.1631-2.2497 | 0.2065 | 131 | 0.1613 | 2606 | 2737 | 96 | 2.2497-2.352 | 0.2259 | 133 | 0.1555 | 2653 | 2786 | 96 | 2.352-2.4759 | 0.2246 | 122 | 0.1628 | 2669 | 2791 | 96 | 2.4759-2.6308 | 0.2277 | 162 | 0.1614 | 2637 | 2799 | 96 | 2.6308-2.8337 | 0.1766 | 130 | 0.1651 | 2632 | 2762 | 96 | 2.8337-3.1183 | 0.1953 | 150 | 0.1681 | 2642 | 2792 | 96 | 3.1183-3.5684 | 0.2037 | 146 | 0.1528 | 2547 | 2693 | 94 | 3.5684-4.4913 | 0.169 | 134 | 0.1404 | 2595 | 2729 | 94 | 4.4913-24.5818 | 0.1947 | 132 | 0.1618 | 2592 | 2724 | 94 |
|
---|
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 | 3.4506 | -2.9362 | -1.412 | 7.4454 | 3.3269 | 3.3641 | 0.0503 | -0.0844 | 0.1332 | 0.0294 | 0.1169 | -0.5178 | -0.256 | 0.269 | -0.2086 | 0.1083 | -0.0259 | -0.0054 | 0.1382 | 0.043 | 0.1322 | 27.526 | -7.5477 | 3.6402 | 2 | 2.1001 | -0.7136 | -0.8659 | 4.5584 | 0.181 | 1.8363 | -0.0265 | -0.073 | -0.1473 | -0.0414 | 0.0648 | -0.0908 | 0.1668 | 0.0735 | -0.0038 | 0.0654 | -0.0074 | -0.0142 | 0.0888 | -0.0114 | 0.0671 | 20.986 | -17.0215 | 3.2138 | 3 | 1.9928 | -0.4408 | 1.1771 | 3.9285 | 0.2732 | 1.0933 | -0.0218 | 0.31 | -0.0777 | -1.2158 | 0.2574 | 0.1799 | 0.0468 | -0.0011 | 0.0025 | 0.3272 | -0.0351 | -0.0336 | 0.1462 | -0.0001 | 0.1453 | 16.6174 | -10.5118 | -12.1953 | 4 | 3.7172 | -0.8473 | -1.57 | 2.5228 | 0.5076 | 4.7207 | -0.1011 | 0.8408 | -0.5611 | -0.5291 | -0.2646 | 0.6821 | 0.6663 | -0.8929 | 0.2957 | 0.3164 | -0.044 | -0.1033 | 0.2697 | -0.0674 | 0.2289 | 11.0877 | -16.464 | -9.8743 | 5 | 3.2913 | 3.1761 | -3.3267 | 2.0009 | -7.0801 | 5.6792 | 0.178 | 0.4093 | 0.3917 | 0.4033 | 0.294 | 0.4003 | -0.5529 | -0.3007 | -0.3679 | 0.1265 | 0.0024 | -0.0161 | 0.1812 | 0.0374 | 0.2423 | 6.3379 | -9.5021 | 4.1357 | 6 | 3.8992 | -3.916 | -0.8238 | 6.0951 | 2.2863 | 4.2745 | -0.2589 | 0.3161 | -0.4564 | 0.021 | 0.0671 | 0.6621 | 0.3747 | -0.2952 | 0.1457 | 0.1092 | -0.045 | -0.012 | 0.1587 | -0.0057 | 0.1749 | 9.7481 | -21.4884 | 2.7762 | 7 | 6.7385 | 2.9876 | -1.1251 | 6.6847 | -3.8992 | 5.9706 | 0.1499 | 0.0699 | -0.1736 | -0.1456 | -0.2598 | 0.0104 | 0.0807 | 0.2978 | 0.1066 | 0.1153 | 0.0156 | 0.0074 | 0.1215 | -0.0197 | 0.0702 | 20.7588 | -19.9027 | -3.938 | 8 | 7.5634 | -5.423 | -2.0245 | 4.5523 | 1.2343 | 4.7996 | 0.0652 | 0.0494 | -0.1948 | -0.6604 | 0.0182 | 0.2734 | -0.1284 | 0.114 | -0.0742 | 0.1704 | -0.0348 | -0.0101 | 0.1158 | 0.0368 | 0.156 | 20.743 | -2.8386 | -9.5617 | 9 | 6.2583 | 4.0723 | 4.6153 | 3.588 | 2.3321 | 4.0065 | -0.0089 | 0.1698 | 0.0859 | -0.4512 | 0.0645 | 0.0728 | -0.008 | 0.1382 | -0.0637 | 0.2282 | 0.0441 | 0.0155 | 0.1663 | 0.0027 | 0.1284 | 20.2406 | 8.5585 | -13.3212 | 10 | 5.441 | -0.5014 | -4.2329 | 4.2882 | 3.7791 | 6.0699 | -0.0115 | 0.5442 | -0.1846 | -0.2779 | -0.2824 | -1.0128 | 0.8919 | 1.0411 | 0.0714 | 0.3395 | 0.0644 | 0.1028 | 0.3907 | 0.0984 | 0.3961 | 36.0322 | 5.4457 | -11.2037 | 11 | 2.725 | 1.385 | 0.6387 | 3.7052 | 3.9901 | 4.7196 | -0.0757 | 0.0318 | -0.1827 | 0.0343 | 0.2087 | -0.3492 | 0.2314 | 0.329 | -0.1869 | 0.1254 | 0.0151 | 0.0169 | 0.1366 | 0.0502 | 0.1462 | 28.1103 | 5.9661 | -4.0643 | 12 | 1.9567 | 0.5362 | 0.9423 | 3.7634 | 0.4642 | 2.0076 | -0.0314 | 0.0952 | 0.093 | 0.0195 | 0.0171 | -0.1564 | -0.1715 | 0.0649 | 0.0484 | 0.0693 | 0.0148 | 0.0175 | 0.0784 | -0.009 | 0.0754 | 20.9824 | 14.6914 | -3.6986 | 13 | 1.2318 | -0.5362 | 0.5853 | 4.3079 | 0.4503 | 4.7326 | -0.0867 | -0.2504 | 0.0269 | 0.8721 | 0.1364 | 0.2906 | -0.1594 | -0.1148 | -0.0312 | 0.2305 | 0.0283 | 0.0641 | 0.1611 | -0.0009 | 0.1331 | 16.3344 | 8.6503 | 11.3024 | 14 | 3.0075 | 0.5811 | 1.2688 | 2.4119 | 0.8243 | 3.2737 | 0.0297 | -0.862 | 0.4365 | 0.5074 | -0.2105 | 0.5658 | -0.4527 | -1.1628 | 0.1654 | 0.2881 | 0.0579 | 0.1229 | 0.2927 | -0.0563 | 0.2155 | 10.293 | 13.7611 | 9.1883 | 15 | 2.9323 | -2.6131 | 1.6023 | 8.9576 | -5.5607 | 4.4577 | 0.3484 | -0.4735 | -0.0406 | -0.5423 | 0.1672 | 0.4754 | 0.4685 | -0.4284 | -0.4536 | 0.1142 | -0.0124 | -0.0031 | 0.1822 | 0.0266 | 0.2212 | 6.2802 | 7.1959 | -4.6172 | 16 | 3.0243 | 2.0561 | 0.133 | 4.6213 | 0.5618 | 4.1679 | -0.2877 | -0.1961 | 0.3805 | 0.0316 | 0.2676 | 0.5246 | -0.345 | -0.2698 | 0.0598 | 0.1214 | 0.045 | 0.022 | 0.1422 | -0.0106 | 0.2164 | 9.7526 | 19.1788 | -3.2688 | 17 | 4.6217 | -0.7607 | 0.2002 | 2.1186 | -3.082 | 4.9039 | 0.0287 | -0.2181 | 0.2007 | 0.2272 | -0.0808 | -0.0386 | -0.1641 | 0.2523 | 0.0623 | 0.1334 | -0.019 | -0.0112 | 0.1459 | -0.0115 | 0.1215 | 20.8106 | 17.7477 | 3.6019 | 18 | 5.2354 | 2.0946 | -2.3351 | 2.1428 | -3.7515 | 7.1111 | 0.0655 | -0.0207 | 0.3103 | 0.2867 | -0.0587 | 0.0318 | -0.2053 | 0.264 | 0.1005 | 0.2064 | 0.0243 | 0.0174 | 0.1651 | 0.0228 | 0.1549 | 21.4873 | 1.0943 | 9.1531 | 19 | 8.5317 | -6.5679 | -5.3089 | 6.7107 | 3.7049 | 4.1317 | 0.0911 | -0.2057 | -0.0803 | 0.4503 | 0.0401 | -0.057 | -0.088 | 0.0429 | -0.1786 | 0.2117 | -0.0335 | -0.0189 | 0.1827 | 0.0165 | 0.1417 | 20.1894 | -10.9052 | 12.8468 | 20 | 2.9686 | 2.8895 | 0.9852 | 3.9811 | 2.5387 | 6.2804 | 0.2244 | -0.1798 | -0.1252 | 0.2456 | -0.0282 | -1.8491 | -0.9279 | 0.9668 | -0.36 | 0.2331 | -0.0394 | -0.0423 | 0.2864 | 0.0312 | 0.5162 | 33.947 | -8.9571 | 9.3417 | 21 | 1.4526 | 0.5187 | -0.5107 | 7.8159 | 3.7785 | 4.7931 | -0.1175 | 0.1521 | 0.0409 | -0.1863 | 0.4735 | -0.6063 | 0.138 | 0.5103 | -0.1913 | 0.1361 | -0.0256 | 0.069 | 0.1916 | 0.0011 | 0.2104 | 19.5379 | 10.4986 | -35.3301 | 22 | 2.8415 | 1.188 | 0.3339 | 5.7533 | -0.144 | 2.583 | -0.0432 | 0.1189 | 0.1842 | -0.0119 | 0.1046 | -0.2304 | -0.1615 | 0.1166 | -0.0615 | 0.1325 | -0.0078 | 0.0116 | 0.1361 | -0.0051 | 0.0797 | 12.9896 | 19.1556 | -32.6891 | 23 | 2.3765 | 0.254 | 0.6054 | 2.8014 | 0.3903 | 4.209 | 0.0198 | -0.1329 | -0.1742 | 0.0513 | 0.1332 | 0.0068 | 0.1521 | -0.1679 | -0.099 | 0.108 | 0.0067 | -0.007 | 0.1348 | 0.0214 | 0.1268 | 8.6206 | 9.2691 | -19.1943 | 24 | 4.6923 | 2.2176 | 2.8127 | 5.0948 | 2.2936 | 6.9967 | -0.0519 | -0.4269 | 0.3582 | 0.2258 | -0.0998 | 0.375 | -0.2836 | -0.8191 | 0.1557 | 0.1013 | 0.0358 | 0.0302 | 0.1846 | 0.0021 | 0.1593 | 2.82 | 16.0536 | -20.2644 | 25 | 3.4831 | -1.1862 | 0.4803 | 2.7505 | -1.7827 | 3.7695 | 0.0745 | -0.1232 | 0.3541 | 0.0555 | 0.0423 | 0.1071 | -0.4468 | -0.0911 | -0.0869 | 0.1457 | -0.0068 | 0.0304 | 0.1061 | -0.0176 | 0.14 | 6.858 | 20.9612 | -28.4641 | 26 | 1.9946 | -0.4947 | -0.5701 | 5.715 | -0.8483 | 1.1799 | 0.2057 | -0.0155 | -0.1818 | 0.583 | 0.0879 | 0.2036 | 0.402 | 0.0073 | -0.2783 | 0.3552 | 0.0478 | -0.0928 | 0.2612 | -0.0342 | 0.1383 | 13.4251 | -4.57 | -23.9693 | 27 | 3.6716 | -1.3744 | -1.4627 | 6.6288 | 5.1013 | 7.2946 | -0.1087 | -0.0724 | -0.0218 | 0.0113 | 0.2478 | -0.3046 | -0.2523 | 0.3961 | -0.1434 | 0.1603 | 0.0344 | -0.052 | 0.2087 | -0.0031 | 0.1935 | 19.5096 | -5.1518 | -30.9672 | 28 | 3.0519 | -1.8089 | -0.2825 | 6.3757 | -0.3025 | 2.3029 | -0.0484 | -0.1113 | -0.2026 | 0.0508 | 0.1136 | -0.2166 | 0.1858 | 0.1307 | -0.0769 | 0.1189 | 0.0187 | -0.0098 | 0.1455 | -0.0116 | 0.0922 | 12.9936 | -13.7888 | -33.9499 | 29 | 3.1053 | -0.5597 | -2.7608 | 3.9425 | 3.3345 | 8.1326 | -0.0904 | 0.1064 | 0.0597 | 0.0562 | 0.2167 | -0.128 | 0.0558 | -0.0009 | -0.0408 | 0.0982 | -0.0126 | -0.0024 | 0.099 | 0.017 | 0.1005 | 9.2891 | -4.6349 | -47.7769 | 30 | 3.9301 | -1.7341 | -2.351 | 4.0431 | 0.9424 | 5.0425 | -0.0612 | 0.6377 | -0.3012 | -0.3399 | -0.0771 | 0.4201 | 0.2158 | -1.0043 | 0.1659 | 0.1201 | -0.037 | -0.0289 | 0.2563 | -0.0096 | 0.1793 | 2.2362 | -10.4421 | -46.4598 | 31 | 3.0832 | 0.8811 | 1.6941 | 6.9227 | -1.191 | 3.5401 | 0.0105 | 0.0058 | -0.2766 | 0.2337 | 0.2742 | 0.4129 | 0.2098 | -0.3197 | -0.2386 | 0.1225 | -0.0423 | 0.0015 | 0.1452 | 0.0479 | 0.1834 | 0.9432 | -15.6157 | -34.6869 | 32 | 4.4925 | 2.2605 | 0.0586 | 2.2299 | -1.7405 | 2.8066 | 0.0674 | 0.1917 | -0.5301 | -0.2679 | -0.0807 | -0.4391 | 0.5369 | 0.3167 | 0.0557 | 0.193 | 0.0688 | -0.0039 | 0.1607 | -0.0312 | 0.1471 | 12.8559 | -15.1991 | -41.5068 | 33 | 1.9555 | 0.4927 | -0.3715 | 4.6686 | -0.4313 | 2.0394 | 0.3076 | 0.0833 | 0.1964 | -0.5768 | 0.0629 | -0.0394 | -0.5344 | -0.0631 | -0.3138 | 0.3619 | -0.0365 | 0.0872 | 0.2746 | -0.0321 | 0.1384 | 13.3826 | 10.0958 | -42.7481 |
|
---|
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 140 through 156 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 157 through 180 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 181 through 196 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 197 through 215 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 216 through 220 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 221 through 231 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 232 through 246 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 247 through 253 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 254 through 264 )A0 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 265 through 271 )A0 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 140 through 156 )B0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 157 through 180 )B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 181 through 197 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|