Software | Name | Classification |
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HKL-2000 | data reductionHKL-2000 | data scalingPHENIX | phasingREFMAC | phasingPHENIX | refinement | | | | |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.495→27.374 Å / SU ML: 0.81 / σ(F): 1.35 / Phase error: 26.48 / Stereochemistry target values: ML / Details: RESIDUES 379-389 ARE DISORDERED.
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2474 | 2710 | 5.1 % |
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Rwork | 0.2014 | - | - |
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obs | 0.2037 | 53119 | 97.17 % |
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.585 Å2 / ksol: 0.345 e/Å3 |
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Displacement parameters | Biso mean: 60.46 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.0127 Å2 | 0 Å2 | -4.8156 Å2 |
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2- | - | 2.2112 Å2 | 0 Å2 |
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3- | - | - | -1.8213 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.495→27.374 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 9269 | 0 | 0 | 30 | 9299 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 9499 | X-RAY DIFFRACTION | f_angle_d0.724 | 12861 | X-RAY DIFFRACTION | f_dihedral_angle_d13.165 | 3525 | X-RAY DIFFRACTION | f_chiral_restr0.051 | 1397 | X-RAY DIFFRACTION | f_plane_restr0.003 | 1648 | | | | | |
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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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2.4951-2.5405 | 0.4195 | 130 | 0.3256 | 2333 | X-RAY DIFFRACTION | 87 | 2.5405-2.5893 | 0.3873 | 131 | 0.3021 | 2638 | X-RAY DIFFRACTION | 96 | 2.5893-2.6421 | 0.304 | 142 | 0.27 | 2619 | X-RAY DIFFRACTION | 97 | 2.6421-2.6995 | 0.3176 | 154 | 0.2751 | 2650 | X-RAY DIFFRACTION | 97 | 2.6995-2.7623 | 0.3207 | 157 | 0.258 | 2581 | X-RAY DIFFRACTION | 97 | 2.7623-2.8313 | 0.3383 | 135 | 0.2502 | 2645 | X-RAY DIFFRACTION | 97 | 2.8313-2.9077 | 0.2713 | 158 | 0.2469 | 2628 | X-RAY DIFFRACTION | 97 | 2.9077-2.9932 | 0.3084 | 127 | 0.2359 | 2643 | X-RAY DIFFRACTION | 97 | 2.9932-3.0897 | 0.3276 | 143 | 0.2451 | 2675 | X-RAY DIFFRACTION | 98 | 3.0897-3.2 | 0.333 | 140 | 0.2388 | 2657 | X-RAY DIFFRACTION | 98 | 3.2-3.3279 | 0.2444 | 158 | 0.2329 | 2644 | X-RAY DIFFRACTION | 98 | 3.3279-3.4791 | 0.2534 | 130 | 0.2184 | 2664 | X-RAY DIFFRACTION | 98 | 3.4791-3.6621 | 0.2779 | 124 | 0.2134 | 2700 | X-RAY DIFFRACTION | 98 | 3.6621-3.8909 | 0.2483 | 146 | 0.2094 | 2705 | X-RAY DIFFRACTION | 98 | 3.8909-4.1904 | 0.2267 | 149 | 0.1843 | 2706 | X-RAY DIFFRACTION | 99 | 4.1904-4.6102 | 0.2052 | 147 | 0.1501 | 2696 | X-RAY DIFFRACTION | 99 | 4.6102-5.2732 | 0.1969 | 133 | 0.1528 | 2749 | X-RAY DIFFRACTION | 99 | 5.2732-6.6281 | 0.2403 | 164 | 0.2061 | 2742 | X-RAY DIFFRACTION | 99 | 6.6281-27.376 | 0.1656 | 142 | 0.1507 | 2734 | X-RAY DIFFRACTION | 96 |
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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 | 1.2734 | -0.0209 | 0.265 | 0.3964 | -0.1424 | 0.1101 | -0.019 | -0.091 | 0.33 | -0.1605 | -0.1354 | -0.0994 | -0.3556 | 0.1444 | 0.3898 | 0.601 | -0.1331 | -0.0034 | 0.2237 | -0.0397 | 0.3104 | 61.7575 | 48.8516 | 5.6234 | 2 | 0.2356 | -0.1514 | -0.1486 | 0.2938 | 0.0062 | 0.1407 | -0.0729 | 0.0292 | -0.0345 | -0.0912 | -0.0745 | 0.1999 | -0.3665 | -0.1006 | -0.8676 | 0.7781 | 0.1834 | -0.1208 | 0.0742 | -0.0048 | 0.2657 | 47.8672 | 49.8721 | -9.0636 | 3 | 0.1119 | 0.1399 | 0.0104 | 0.2124 | 0.1089 | 0.3481 | -0.0607 | 0.1693 | -0.011 | -0.1841 | -0.1123 | 0.0045 | -0.3276 | 0.1857 | -0.5831 | 0.6295 | -0.0531 | 0.0721 | -0.0064 | 0.1365 | -0.0105 | 57.0145 | 42.705 | -6.224 | 4 | 0.2541 | 0.0876 | 0.0897 | 0.2208 | 0.0409 | 0.4292 | -0.0761 | -0.1354 | -0.0747 | -0.1886 | -0.0024 | 0.0646 | -0.2754 | 0.2725 | -0.0019 | 0.4505 | -0.0171 | -0.0012 | 0.1727 | -0.0212 | 0.2585 | 60.798 | 36.5304 | 0.6243 | 5 | 0.3831 | -0.1024 | 0.3611 | 0.1864 | -0.1374 | 0.404 | -0.1515 | -0.0268 | 0.0259 | 0.0354 | -0.0317 | -0.1692 | -0.4036 | 0.3692 | -0.0262 | 0.2642 | -0.1258 | -0.011 | 0.2419 | 0.0325 | 0.2075 | 72.3243 | 37.936 | 19.5833 | 6 | 0.2393 | -0.0583 | -0.1054 | 0.1439 | 0.0809 | 0.1759 | -0.0083 | -0.1189 | -0.2536 | 0.0065 | 0.0561 | 0.0445 | -0.1817 | 0.0163 | -0 | 0.4217 | -0.0685 | -0.1075 | 0.3834 | 0.0088 | 0.366 | 73.7967 | 34.2721 | 34.4301 | 7 | 0.0768 | 0.1102 | 0.0699 | 0.1404 | 0.0882 | 0.0551 | -0.1023 | 0.0387 | 0.0627 | -0.1069 | -0.097 | 0.0279 | 0.0357 | -0.0923 | 0 | 0.5177 | 0.0521 | -0.0815 | 0.2094 | -0.047 | 0.2968 | 45.1257 | 38.7533 | -14.4178 | 8 | 0.0363 | -0.0113 | 0.0048 | 0.0209 | 0.0006 | 0.0007 | 0.001 | 0.015 | 0.0439 | -0.0547 | 0.1531 | -0.1074 | 0.0449 | 0.0061 | -0.0008 | 0.7807 | -0.1097 | -0.1573 | 0.4677 | 0.0909 | 0.5541 | 65.5332 | 55.9899 | -4.0132 | 9 | 0.2696 | -0.1088 | -0.062 | 0.223 | 0.1538 | 0.425 | -0.2796 | -0.1105 | 0.0429 | 0.2537 | 0.1155 | -0.1289 | -0.215 | -0.2386 | -0.0942 | 0.5201 | 0.1119 | -0.0154 | 0.5274 | 0.1053 | 0.5536 | 15.504 | 38.4409 | 60.5702 | 10 | 0.0247 | 0.0142 | -0.0138 | 0.0644 | 0.0558 | 0.0665 | -0.1287 | -0.3693 | 0.1927 | 0.2848 | -0.0376 | -0.0022 | -0.1887 | -0.1194 | -0.0001 | 0.6017 | 0.1347 | 0.0545 | 0.6511 | -0.0692 | 0.5019 | 11.7756 | 34.4642 | 77.1558 | 11 | 0.0138 | -0.0001 | -0.0105 | 0.0187 | 0.0088 | 0.0121 | 0.1708 | 0.1712 | -0.0138 | 0.1758 | 0.2593 | -0.0132 | 0.2385 | 0.0429 | -0.0007 | 0.6421 | 0.0504 | 0.0569 | 0.8502 | 0.0829 | 0.6942 | 6.7205 | 15.2374 | 77.9797 | 12 | 0.151 | -0.2012 | 0.1975 | 0.3039 | -0.1336 | 0.5732 | -0.1118 | -0.1404 | -0.0007 | 0.1955 | 0.13 | 0.0412 | -0.0683 | -0.2884 | -0.0001 | 0.2346 | 0.0152 | 0.0635 | 0.4033 | 0.0546 | 0.4849 | 15.0418 | 31.0677 | 62.5958 | 13 | 0.1379 | -0.1485 | 0.0774 | 0.1664 | -0.1448 | 0.4655 | -0.0714 | 0.0193 | -0.1281 | -0.0128 | -0.0359 | -0.078 | 0.1683 | -0.0544 | 0 | 0.2672 | -0.0737 | 0.0201 | 0.3764 | 0.0361 | 0.4101 | 24.6334 | 28.1637 | 48.5841 | 14 | 0.1192 | 0.0925 | -0.0439 | 0.0908 | -0.1375 | 0.5622 | -0.0139 | 0.0947 | 0.0206 | -0.1565 | 0.0547 | 0.0972 | -0.1261 | -0.3416 | 0.003 | 0.3118 | 0.0162 | 0.0054 | 0.4755 | 0.0585 | 0.4682 | 27.4101 | 34.0754 | 36.73 | 15 | 0.4071 | 0.1937 | 0.2243 | 0.2588 | -0.1448 | 0.4698 | -0.0674 | 0.0372 | 0.0409 | 0.0572 | 0.1017 | 0.2305 | 0.024 | 0.0032 | -0 | 0.4136 | -0.0152 | 0.0828 | 0.3407 | 0.0489 | 0.4442 | 38.1403 | 35.2392 | 33.9248 | 16 | 0.165 | 0.1747 | 0.1379 | 0.188 | 0.1509 | 0.1203 | 0.2118 | -0.1317 | 0.2144 | 0.0108 | 0.0864 | -0.0181 | -0.0877 | -0.2745 | 0.1571 | 0.3259 | 0.0546 | 0.1654 | 0.4165 | 0.1933 | 0.4011 | 12.4051 | 27.8304 | 73.3163 | 17 | 0.2694 | 0.4669 | -0.4367 | 1.3296 | -0.2894 | 1.1681 | 0.3024 | -0.0722 | 0.331 | 0.0476 | -0.0219 | 0.2037 | -0.2523 | -0.0642 | 0.5666 | 0.3038 | 0.1093 | -0.0034 | 0.6186 | -0.1964 | 0.4037 | 90.5025 | 37.8232 | 73.9482 | 18 | 0.0255 | 0.0318 | -0.0234 | 0.0396 | -0.0305 | 0.0387 | 0.0933 | -0.0678 | 0.2207 | -0.1645 | -0.1298 | -0.0369 | -0.2885 | 0.3109 | -0 | 0.4014 | -0.0578 | -0.0456 | 0.5227 | -0.163 | 0.5989 | 114.8717 | 39.3264 | 70.0183 | 19 | 0.4226 | 0.2733 | -0.0195 | 0.2158 | -0.1007 | 0.3922 | -0.0521 | -0.4679 | 0.167 | 0.0288 | 0.0175 | -0.0073 | -0.0483 | 0.0392 | -0.0001 | 0.2392 | 0.0333 | -0.0525 | 0.4408 | -0.0478 | 0.3848 | 99.7995 | 33.828 | 69.3552 | 20 | 0.499 | 0.0132 | -0.2478 | 0.2515 | 0.143 | 0.2088 | -0.1762 | -0.2374 | -0.0681 | 0.0388 | 0.1395 | -0.0543 | -0.1809 | -0.0398 | 0.0001 | 0.262 | 0.0425 | -0.0385 | 0.3822 | 0.016 | 0.368 | 87.958 | 28.2082 | 66.7482 | 21 | 0.2767 | 0.1249 | -0.1322 | 0.1952 | 0.0599 | 0.1582 | 0.0226 | -0.2501 | -0.1237 | 0.0568 | -0.0034 | 0.0481 | 0.051 | -0.1587 | -0.0001 | 0.3024 | -0.0065 | 0.0125 | 0.4608 | 0.0537 | 0.3113 | 73.6574 | 26.5567 | 66.1938 | 22 | 0.5273 | 0.1774 | -0.1525 | 0.4302 | 0.0301 | 0.299 | -0.0242 | -0.5416 | 0.189 | 0.1358 | 0.0674 | 0.0938 | -0.0413 | -0.0337 | -0.0524 | 0.2788 | 0.061 | 0.0414 | 0.6562 | -0.007 | 0.2707 | 64.8199 | 29.7881 | 70.8401 | 23 | 0.2409 | -0.1256 | -0.0989 | 0.1685 | 0.0013 | 0.2706 | -0.256 | -0.1372 | 0.0795 | 0.0307 | 0.2657 | -0.0249 | -0.0938 | -0.2782 | 0 | 0.3713 | 0.1153 | 0.0516 | 0.5527 | 0.05 | 0.6148 | 56.1115 | 30.9364 | 63.9706 | 24 | 0.1217 | 0.0601 | -0.0318 | 0.3263 | -0.2732 | 0.2274 | -0.1265 | -0.1699 | 0.1291 | -0.0139 | -0.015 | 0.026 | -0.016 | 0.1335 | -0.0062 | 0.1524 | 0.0374 | -0.0165 | 0.4486 | -0.1804 | 0.299 | 105.2556 | 31.4132 | 65.8978 |
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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 -3:19) | 2 | X-RAY DIFFRACTION | 2 | (CHAIN A AND RESID 20:67)3 | X-RAY DIFFRACTION | 3 | (CHAIN A AND RESID 68:137)4 | X-RAY DIFFRACTION | 4 | (CHAIN A AND RESID 138:182)5 | X-RAY DIFFRACTION | 5 | (CHAIN A AND RESID 183:307)6 | X-RAY DIFFRACTION | 6 | (CHAIN A AND RESID 308:351)7 | X-RAY DIFFRACTION | 7 | (CHAIN A AND RESID 352:378)8 | X-RAY DIFFRACTION | 8 | (CHAIN A AND RESID 390:401)9 | X-RAY DIFFRACTION | 9 | (CHAIN B AND RESID -1:20) | 10 | X-RAY DIFFRACTION | 10 | (CHAIN B AND RESID 21:70)11 | X-RAY DIFFRACTION | 11 | (CHAIN B AND RESID 71:83)12 | X-RAY DIFFRACTION | 12 | (CHAIN B AND RESID 84:168)13 | X-RAY DIFFRACTION | 13 | (CHAIN B AND RESID 169:230)14 | X-RAY DIFFRACTION | 14 | (CHAIN B AND RESID 231:298)15 | X-RAY DIFFRACTION | 15 | (CHAIN B AND RESID 299:349)16 | X-RAY DIFFRACTION | 16 | (CHAIN B AND RESID 350:398)17 | X-RAY DIFFRACTION | 17 | (CHAIN C AND RESID 2:18)18 | X-RAY DIFFRACTION | 18 | (CHAIN C AND RESID 19:45)19 | X-RAY DIFFRACTION | 19 | (CHAIN C AND RESID 46:135)20 | X-RAY DIFFRACTION | 20 | (CHAIN C AND | | | | | | | | | | | | | | | | | |
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