Software | Name | Version | Classification |
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SBC-Collect | | data collectionSHELXD | | phasingMLPHARE | | phasingDM | | model buildingARP | | model buildingWARP | | model buildingHKL-3000 | | phasingPHENIX | (phenix.refine: 1.7.1_743)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingDM | | phasing | | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.137→45.893 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2181 | 3711 | 5.05 % | random |
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Rwork | 0.1679 | - | - | - |
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all | 0.1705 | 73465 | - | - |
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obs | 0.1705 | 73465 | 98.58 % | - |
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.568 Å2 / ksol: 0.333 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.5757 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 5.0944 Å2 | 0 Å2 |
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3- | - | - | -1.5187 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.137→45.893 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10347 | 0 | 71 | 394 | 10812 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 10723 | X-RAY DIFFRACTION | f_angle_d1.072 | 14559 | X-RAY DIFFRACTION | f_dihedral_angle_d14.119 | 3874 | X-RAY DIFFRACTION | f_chiral_restr0.073 | 1549 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1887 | | | | | |
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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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2.1367-2.1637 | 0.3036 | 121 | 0.2079 | 2185 | X-RAY DIFFRACTION | 86 | 2.1637-2.1922 | 0.2687 | 112 | 0.2062 | 2415 | X-RAY DIFFRACTION | 92 | 2.1922-2.2222 | 0.2841 | 126 | 0.2024 | 2435 | X-RAY DIFFRACTION | 94 | 2.2222-2.254 | 0.3087 | 122 | 0.2057 | 2501 | X-RAY DIFFRACTION | 96 | 2.254-2.2876 | 0.2426 | 135 | 0.204 | 2520 | X-RAY DIFFRACTION | 98 | 2.2876-2.3233 | 0.2903 | 135 | 0.2043 | 2588 | X-RAY DIFFRACTION | 99 | 2.3233-2.3614 | 0.3199 | 152 | 0.2125 | 2556 | X-RAY DIFFRACTION | 100 | 2.3614-2.4022 | 0.2532 | 149 | 0.199 | 2611 | X-RAY DIFFRACTION | 100 | 2.4022-2.4458 | 0.2927 | 124 | 0.196 | 2568 | X-RAY DIFFRACTION | 100 | 2.4458-2.4929 | 0.2521 | 126 | 0.1949 | 2626 | X-RAY DIFFRACTION | 100 | 2.4929-2.5438 | 0.2782 | 135 | 0.1914 | 2617 | X-RAY DIFFRACTION | 100 | 2.5438-2.5991 | 0.2526 | 133 | 0.1881 | 2611 | X-RAY DIFFRACTION | 100 | 2.5991-2.6595 | 0.276 | 132 | 0.1881 | 2572 | X-RAY DIFFRACTION | 100 | 2.6595-2.726 | 0.2668 | 130 | 0.1893 | 2638 | X-RAY DIFFRACTION | 100 | 2.726-2.7997 | 0.271 | 131 | 0.1853 | 2595 | X-RAY DIFFRACTION | 100 | 2.7997-2.8821 | 0.2272 | 146 | 0.1866 | 2600 | X-RAY DIFFRACTION | 100 | 2.8821-2.9751 | 0.2436 | 127 | 0.1943 | 2605 | X-RAY DIFFRACTION | 100 | 2.9751-3.0814 | 0.2783 | 145 | 0.1966 | 2611 | X-RAY DIFFRACTION | 100 | 3.0814-3.2047 | 0.2371 | 129 | 0.1862 | 2640 | X-RAY DIFFRACTION | 100 | 3.2047-3.3506 | 0.2293 | 159 | 0.1817 | 2612 | X-RAY DIFFRACTION | 100 | 3.3506-3.5271 | 0.2229 | 158 | 0.1745 | 2601 | X-RAY DIFFRACTION | 100 | 3.5271-3.748 | 0.2066 | 119 | 0.1583 | 2639 | X-RAY DIFFRACTION | 100 | 3.748-4.0373 | 0.176 | 147 | 0.1365 | 2650 | X-RAY DIFFRACTION | 100 | 4.0373-4.4433 | 0.1713 | 138 | 0.1228 | 2661 | X-RAY DIFFRACTION | 100 | 4.4433-5.0855 | 0.1615 | 145 | 0.1192 | 2680 | X-RAY DIFFRACTION | 100 | 5.0855-6.4044 | 0.1759 | 162 | 0.1698 | 2664 | X-RAY DIFFRACTION | 100 | 6.4044-45.9035 | 0.1767 | 173 | 0.1543 | 2753 | X-RAY DIFFRACTION | 98 |
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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 | 1.5391 | 0.0563 | -0.337 | 0.0798 | -0.0116 | 0.4873 | 0.0238 | -0.1775 | -0.0554 | 0.0632 | 0.0216 | -0.034 | 0.1211 | -0.0268 | -0.0415 | 0.2959 | -0.0192 | -0.0237 | 0.3015 | 0.0671 | 0.3024 | 50.3802 | 99.8423 | 30.9961 | 2 | 2.2636 | -0.3512 | -0.6946 | 1.577 | -0.5122 | 1.6771 | -0.0855 | -0.2748 | -0.2204 | 0.1791 | 0.0083 | -0.0546 | 0.1028 | 0.0876 | 0.0815 | 0.2485 | -0.027 | -0.0224 | 0.3098 | 0.0527 | 0.2156 | 46.8606 | 97.352 | 40.7743 | 3 | 1.219 | -1.0042 | 0.3953 | 3.1355 | -0.0783 | 0.9784 | -0.0163 | -0.0532 | 0.0316 | 0.1944 | 0.0767 | -0.0862 | -0.05 | -0.0425 | -0.0829 | 0.2179 | -0.0112 | 0.0101 | 0.2943 | 0.0009 | 0.2437 | 64.3142 | 123.9245 | 32.6217 | 4 | 1.2713 | -0.8522 | 0.2744 | 2.0504 | 0.0861 | 1.0517 | 0.0381 | -0.1529 | 0.0648 | -0.0051 | 0.0235 | -0.0249 | -0.1307 | -0.0253 | -0.0201 | 0.2052 | -0.01 | 0.0113 | 0.2972 | 0.022 | 0.2528 | 54.8679 | 132.8987 | 26.07 | 5 | 1.6775 | 0.5615 | -0.3613 | 0.4291 | -0.0334 | 1.4164 | -0.0346 | -0.1131 | -0.0429 | 0.0156 | -0.0094 | -0.0001 | -0.0284 | -0.0214 | 0.0399 | 0.2135 | 0.0168 | -0.0149 | 0.2336 | 0.0063 | 0.234 | 49.9686 | 120.3972 | 20.1411 | 6 | 2.6713 | -1.117 | -0.6295 | 1.7211 | -1.3465 | 2.5714 | 0.1003 | 0.0035 | -0.0983 | 0.148 | 0.1911 | 0.1418 | -0.358 | -0.1462 | -0.2544 | 0.2348 | -0.0384 | 0.0208 | 0.2176 | 0.0231 | 0.2623 | 48.9381 | 104.8413 | 17.1926 | 7 | 1.7988 | -0.0219 | 0.7562 | 1.4912 | 0.9692 | 3.9203 | 0.0106 | -0.0257 | -0.2022 | 0.0347 | -0.007 | 0.0421 | 0.2184 | -0.0313 | -0.0212 | 0.1988 | 0.021 | -0.0054 | 0.1743 | 0.0265 | 0.2697 | 53.22 | 97.5472 | 15.23 | 8 | 2.2163 | -1.0458 | -0.383 | 3.5474 | 0.4906 | 2.6232 | -0.3501 | 0.3596 | -0.4988 | 0.1105 | 0.2211 | 0.5465 | 0.6992 | -0.1381 | 0.243 | 0.4003 | -0.0907 | 0.0276 | 0.3585 | 0.0047 | 0.3626 | 18.2492 | 86.9747 | 20.2609 | 9 | 0.6584 | -0.0933 | -0.0821 | 0.4808 | 0.2977 | 1.6159 | -0.0372 | 0.1393 | -0.0325 | -0.0604 | 0.0161 | 0.1511 | 0.0254 | -0.145 | 0.0248 | 0.23 | -0.0031 | -0.0153 | 0.3023 | 0.0275 | 0.2976 | 3.5659 | 107.1908 | 13.259 | 10 | 2.4969 | 1.1501 | -0.2389 | 4.499 | -1.149 | 2.9067 | 0.0745 | -0.1645 | 0.4107 | 0.0701 | -0.0391 | 0.4867 | -0.3357 | -0.5354 | -0.0268 | 0.271 | 0.0886 | 0.0078 | 0.3317 | -0.0422 | 0.3053 | 4.1467 | 128.631 | 36.1915 | 11 | 1.5401 | -0.1378 | 0.5966 | 0.3858 | 0.695 | 2.5281 | -0.012 | -0.0477 | 0.2476 | -0.0327 | 0.0236 | -0.0065 | -0.3795 | 0.1065 | -0.0243 | 0.2839 | -0.0345 | 0.028 | 0.2884 | 0.0153 | 0.2621 | 16.8602 | 127.4753 | 26.3249 | 12 | 0.4577 | 0.0676 | 0.1002 | 1.179 | 0.3512 | 0.5646 | -0.0429 | -0.037 | -0.0133 | -0.0534 | 0.0362 | -0.0668 | 0.0216 | -0.0462 | 0.0184 | 0.2368 | -0.0109 | 0.0227 | 0.2804 | 0.0209 | 0.2308 | 23.8787 | 105.1856 | 25.572 | 13 | 0.8796 | -0.2415 | 0.4252 | 0.1953 | -0.2988 | 0.442 | -0.049 | -0.0831 | 0.0491 | -0.0143 | -0.0833 | 0.0481 | 0.1459 | 0.0791 | 0.1598 | 0.3496 | 0.0186 | 0.0401 | 0.2876 | -0.0199 | 0.2513 | 42.5027 | 106.2845 | -11.1335 | 14 | 1.2858 | -0.4995 | -0.2662 | 0.808 | 0.0419 | 2.5203 | 0.1326 | 0.0765 | 0.1884 | -0.3334 | 0.1262 | -0.2799 | -0.0905 | 0.5706 | 0.0157 | 0.2695 | -0.0261 | 0.0486 | 0.4131 | -0.0225 | 0.2938 | 62.7813 | 112.4031 | -7.0303 | 15 | 1.7116 | -0.8838 | 0.4592 | 1.3208 | 0.0158 | 0.9312 | 0.1063 | 0.231 | -0.1899 | -0.212 | 0.0023 | -0.1497 | 0.213 | 0.1163 | -0.0794 | 0.2786 | 0.0063 | 0.0263 | 0.3201 | -0.0274 | 0.3013 | 49.4909 | 102.476 | -15.2028 | 16 | 0.4568 | -0.2734 | 0.3045 | 2.383 | 0.9845 | 1.1799 | -0.0015 | 0.1391 | 0.0236 | -0.2617 | 0.1709 | -0.3516 | -0.0029 | 0.2828 | -0.0422 | 0.2718 | 0.0074 | 0.0531 | 0.3687 | 0.0221 | 0.2644 | 36.8093 | 126.2119 | -16.9753 | 17 | 1.1683 | 0.0144 | 0.3444 | 1.5254 | 0.0302 | 0.8002 | -0.0694 | 0.0162 | 0.2289 | -0.0253 | 0.0182 | -0.1278 | -0.0964 | 0.1498 | 0.0654 | 0.2401 | 0.0198 | -0.0045 | 0.2872 | 0.0209 | 0.2688 | 33.3156 | 137.7758 | -11.6693 | 18 | 1.7815 | -0.9246 | 0.3694 | 1.1332 | -0.5617 | 0.673 | -0.0726 | 0.0221 | 0.0783 | 0.1083 | 0.0065 | -0.0514 | -0.0701 | 0.0433 | -0.0014 | 0.2139 | 0.0076 | 0.0185 | 0.2403 | 0.0174 | 0.1983 | 35.8416 | 128.4895 | -2.7845 | 19 | 1.1946 | -0.6127 | 0.0419 | 2.2122 | 0.1631 | 1.1008 | -0.046 | 0.0117 | -0.0874 | 0.1411 | 0.0573 | 0.0115 | 0.1278 | 0.0341 | -0.0048 | 0.2146 | -0.0144 | -0 | 0.2283 | -0.0072 | 0.182 | 28.2961 | 115.2265 | 0.1954 | 20 | 2.9064 | 0.5151 | -0.4891 | 1.2801 | -0.5048 | 2.2968 | -0.0454 | 0.3025 | -0.1129 | -0.0417 | 0.0278 | 0.0299 | 0.0846 | -0.1246 | 0.0251 | 0.2365 | 0.0111 | -0.0015 | 0.2051 | -0.0395 | 0.1935 | 27.8579 | 101.3131 | -6.5603 |
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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 (resseq 6:54)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 55:145)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 146:208)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 209:245)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 246:348)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 349:377)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 378:431)8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq 1:23)9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 24:173)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 174:208)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 209:298)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 299:431)13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resseq 6:53)14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resseq 54:82)15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resseq 83:145)16 | X-RAY DIFFRACTION | 16 | chain 'C' and (resseq 146:173)17 | X-RAY DIFFRACTION | 17 | chain 'C' and (resseq 174:245)18 | X-RAY DIFFRACTION | 18 | chain 'C' and ( | | | | | | | | | | | | | | | | | |
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