Software Name Version Classification SBC-Collectdata collection HKL-3000phasing SHELXmodel building ARP/wARPmodel building MOLREPphasing PHENIX(phenix.refine: 1.7_650)refinement HKL-3000data reduction HKL-3000data scaling SHELXphasing
Refinement Method to determine structure : SAD / Resolution : 2.012→36.801 Å / SU ML : 0.24 / σ(F) : 0 / Phase error : 20.59 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2108 2646 5.07 % Rwork 0.1602 - - obs 0.1629 52175 86.86 % all - 54821 -
Solvent computation Shrinkage radii : 0.95 Å / VDW probe radii : 1.2 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 42.67 Å2 / ksol : 0.388 e/Å3 Displacement parameters Baniso -1 Baniso -2 Baniso -3 1- 5.0891 Å2 -0 Å2 -0 Å2 2- - -2.0805 Å2 0 Å2 3- - - -3.0086 Å2
Refinement step Cycle : LAST / Resolution : 2.012→36.801 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6485 0 26 622 7133
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.008 6653 X-RAY DIFFRACTION f_angle_d1.251 9028 X-RAY DIFFRACTION f_dihedral_angle_d13.514 2452 X-RAY DIFFRACTION f_chiral_restr0.089 1026 X-RAY DIFFRACTION f_plane_restr0.007 1175
LS refinement shell Show large table (7 x 19) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.0123-2.0489 0.2903 120 0.2173 1994 X-RAY DIFFRACTION 67 2.0489-2.0883 0.3216 117 0.1993 2390 X-RAY DIFFRACTION 81 2.0883-2.1309 0.2848 127 0.1981 2446 X-RAY DIFFRACTION 83 2.1309-2.1773 0.2546 133 0.1765 2499 X-RAY DIFFRACTION 84 2.1773-2.2279 0.2396 153 0.174 2465 X-RAY DIFFRACTION 84 2.2279-2.2836 0.2118 130 0.1647 2533 X-RAY DIFFRACTION 85 2.2836-2.3453 0.2425 140 0.1633 2554 X-RAY DIFFRACTION 86 2.3453-2.4143 0.2342 132 0.1628 2573 X-RAY DIFFRACTION 87 2.4143-2.4923 0.2347 123 0.1636 2642 X-RAY DIFFRACTION 88 2.4923-2.5813 0.2357 142 0.1729 2630 X-RAY DIFFRACTION 88 2.5813-2.6846 0.2283 134 0.1648 2700 X-RAY DIFFRACTION 90 2.6846-2.8068 0.2234 138 0.1632 2701 X-RAY DIFFRACTION 91 2.8068-2.9547 0.2145 146 0.17 2718 X-RAY DIFFRACTION 91 2.9547-3.1397 0.1988 153 0.1618 2772 X-RAY DIFFRACTION 92 3.1397-3.382 0.219 152 0.1588 2803 X-RAY DIFFRACTION 93 3.382-3.722 0.2123 146 0.1448 2786 X-RAY DIFFRACTION 92 3.722-4.2599 0.1606 153 0.1322 2787 X-RAY DIFFRACTION 91 4.2599-5.3644 0.1357 147 0.1259 2746 X-RAY DIFFRACTION 89 5.3644-36.807 0.2228 160 0.1814 2790 X-RAY DIFFRACTION 87
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 48) Hide large table 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 0.1293 0.1774 0.0654 0.3122 0.2082 0.2788 0.0687 0.0678 0.0587 0.0185 -0.0864 0.0587 0.0922 0.0434 0.028 0.0473 0.015 -0.013 0.0672 0.0006 0.0767 34.7296 38.8774 -17.7575 2 0.1526 0.04 -0.0071 0.0366 -0.0223 0.0888 -0.0178 0.0041 0.0578 0.0029 -0.0083 0.0189 -0.109 0.0538 0.0132 0.0869 -0.03 -0.005 0.0879 -0.0059 0.0701 43.9304 47.5404 -10.1374 3 0.3972 0.116 0.0753 0.1117 0.1734 0.3712 0.1119 -0.0027 -0.0223 -0.0913 0.0016 0.0127 -0.2129 -0.0029 -0.0458 0.1534 -0.0105 0.0279 0.0832 -0.0047 0.0954 41.3451 55.6125 -21.2414 4 0.1426 0.036 0.0179 0.0568 0.0743 0.1079 0.0875 -0.0071 -0.027 0.083 -0.0138 -0.0381 -0.0647 0.0019 -0.0318 0.0859 0.0042 0.0264 0.0585 0.0201 0.0921 36.0232 34.4075 -10.2501 5 0.0842 0.0029 0.0047 0.0298 -0.0851 0.2764 0.0387 -0.0502 -0.1372 0.0807 -0.0941 0.0234 0.05 0.025 0.0217 0.1256 -0.0149 0.0161 0.0686 0.0108 0.1201 39.0211 31.8372 -8.8992 6 0.1827 -0.1934 0.0102 0.2049 0.0032 0.4163 -0.0134 -0.0143 0.0664 -0.0436 -0.1204 -0.0739 -0.0605 -0.0145 0.0237 0.1095 -0.0465 0.0064 0.0597 -0.0145 0.1228 43.4099 59.3072 -8.0442 7 0.1932 0.064 0.0677 0.3549 0.0369 0.032 0.0534 -0.0335 0.0488 -0.0549 -0.0762 0.0728 0.0294 -0.0784 0.0037 0.1223 -0.0195 0.0032 0.0909 0.0104 0.099 37.4931 46.9217 -15.2816 8 0.3303 0.0698 0.0185 0.1083 -0.0476 0.4036 -0.0799 0.0626 -0.107 -0.0149 -0.0545 -0.1154 0.1521 0.1172 0.0307 0.1308 0.0227 0.0091 0.1161 0.0001 0.1268 49.738 35.9067 -20.2156 9 0.1893 0.1598 -0.1104 0.5205 0.1051 0.2936 -0.1007 -0.0472 -0.0097 -0.0764 -0.0006 -0.056 -0.0249 0.0425 0.0535 0.1348 -0.0137 -0.0109 0.1225 0.0427 0.1925 55.3706 47.7706 -23.7037 10 0.0985 0.0091 0.0582 0.0771 0.0632 0.0738 0.0196 0.0418 -0.0328 0.0329 -0.0413 0.0065 0.0212 0.0561 -0.0342 0.0637 -0.0016 -0.0104 0.08 0.0151 0.0655 43.3158 39.7488 -8.3957 11 0.3193 0.0408 0.1833 1.0677 0.3024 0.1781 0.0043 0.2182 0.0132 -0.2558 -0.0151 -0.0236 -0.1111 0.1082 -0.0254 0.1441 0.0418 0.0114 0.1927 -0.0108 0.0635 47.8208 45.2584 -27.9717 12 0.0647 0.0153 -0.0004 0.0667 0.0024 0.0001 0.0126 0.1282 0.0332 -0.0744 0.0673 0.0289 0.0486 0.0003 -0.0352 0.1755 0.0556 -0.0386 0.2655 -0.0039 0.1043 43.3626 47.3451 -30.6116 13 0.4704 0.147 0.6367 0.2003 0.1882 1.1335 -0.1256 0.0817 0.0499 -0.0239 -0.0266 0.0173 -0.1383 0.0773 -0.1103 0.088 -0.0153 -0.1254 0.1517 -0.1447 0.2725 26.0726 25.0066 23.022 14 0.2638 0.0644 -0.0049 0.0487 0.0769 0.1772 0.0022 0.0075 -0.0629 0.062 0.001 -0.0499 0.082 -0.0489 0.0214 0.1613 -0.0338 0.0068 0.1095 -0.0215 0.0852 37.414 27.0986 32.9888 15 0.0713 0.0596 -0.0073 0.0524 -0.0153 0.0355 0.009 0.0224 -0.0084 0.0241 0.0137 -0.0036 0.025 0.0127 -0.0247 0.7005 -0.1982 -0.015 0.751 -0.0554 0.4785 44.9919 13.9935 43.6208 16 0.0739 -0.0697 0.0548 0.0998 -0.0479 0.0452 -0.0266 -0.0646 -0.0072 0.0277 0.0258 -0.0169 -0.0091 0.0575 0.0053 0.36 0.0682 -0.1116 0.4019 -0.0284 0.2349 48.6103 27.7606 45.962 17 0.1194 0.0053 0.0051 0.0573 0.0401 0.0937 -0.1117 0.0135 -0.0506 -0.0503 -0.0326 0.0338 -0.0049 -0.0854 -0.005 0.1013 -0.0333 0.0234 0.1256 -0.0446 0.1266 38.1932 20.7178 24.7292 18 0.0376 0.0652 0.021 0.1915 -0.0632 0.2187 -0.0437 -0.0386 -0.0056 -0.0478 0.024 0.1255 0.1248 0.0277 -0.0049 0.1156 -0.0362 0.0481 0.1565 -0.0336 0.1235 39.9397 18.7448 29.5911 19 0.257 -0.2338 -0.267 0.5417 0.1508 0.4644 -0.0468 0.0659 -0.028 0.1252 -0.0207 0.0111 0.015 -0.1607 0.0323 0.1147 0.0309 0.0136 0.152 -0.0637 0.1623 32.3655 38.0449 40.7804 20 0.3162 -0.0878 -0.1086 0.1109 0.0509 0.1992 -0.0394 0.0054 0.0115 0.1197 -0.045 0.0628 0.1601 -0.0476 0.0473 0.1432 -0.0089 0.0436 0.1334 -0.017 0.1826 45.2101 16.9946 31.602 21 0.0331 0.069 0.0731 0.2136 0.0812 0.2573 -0.0889 0.0311 0.0435 0.0368 -0.0637 0.1649 0.0241 0.0052 -0.008 0.0792 -0.0155 0.042 0.1185 -0.0327 0.1409 42.1985 21.8087 29.1855 22 0.2197 0.0849 0.0415 0.1557 -0.0208 0.3082 0.0368 -0.0739 -0.0819 0.0244 -0.0101 -0.0093 0.1658 -0.0918 0.0554 0.274 -0.1226 0.144 0.2295 -0.0527 0.2011 30.3682 12.4638 38.7652 23 0.2231 -0.0954 -0.0229 0.1939 0.1248 0.1497 -0.0473 -0.0833 0.0698 0.0964 0.0498 -0.0476 0.1806 -0.0988 0.0258 0.1162 -0.0183 0.0126 0.1126 -0.0357 0.0793 38.484 25.8707 38.6322 24 0.0899 0.0586 -0.0265 0.0457 -0.0376 0.0569 0.0284 0.0045 -0.0125 0.0575 -0.0128 0.0258 0.0624 -0.0533 0.0781 0.2171 -0.1323 0.107 0.1716 -0.0757 0.1798 30.5385 8.6008 27.7621 25 0.0509 -0.0323 -0.0353 0.0806 0.0371 0.0714 0.0255 0.0223 0.0261 -0.0764 -0.0291 -0.0385 0.0248 0.0285 0.0075 0.0847 0.0198 0.006 0.0838 0.0088 0.0701 47.308 41.0384 15.7249 26 0.9341 0.0656 0.3763 0.9908 0.1192 0.1601 0.0055 -0.0682 -0.0215 0.3071 -0.0237 -0.2019 -0.0271 -0.0594 -0.0195 0.1355 -0.0073 -0.0273 0.2003 -0.0054 0.1236 69.0609 31.4542 27.0582 27 0.1793 -0.0513 0.0148 0.2502 0.0048 0.1603 0.04 -0.0454 0.0463 -0.0852 -0.0365 0.0238 0.0334 0.043 -0.0076 0.099 -0.003 0.0113 0.0847 -0.012 0.0877 52.9554 35.3373 23.3515 28 0.0789 -0.0991 -0.0485 0.2151 -0.0141 0.1524 -0.0295 0.0144 -0.0023 0.2091 -0.0525 0.1147 -0.0498 0.0258 0.0135 0.171 -0.007 0.0174 0.1209 -0.016 0.1011 55.2932 42.6018 28.3464 29 0.1428 -0.0505 0.0487 0.176 -0.2057 0.3029 -0.033 0.0767 -0.0276 -0.0745 -0.0796 0.0605 0.0827 0.1049 0.0131 0.1748 0.0007 -0.026 0.0935 -0.0031 0.0698 50.5626 25.6009 6.6193 30 0.3262 -0.0639 -0.1246 0.5612 -0.1833 0.1293 0.0086 -0.18 -0.0881 0.1396 0.0137 0.018 -0.059 0.0407 -0.0203 0.0668 -0.014 -0.006 0.1098 -0.0108 0.1008 55.2259 39.2457 14.8311 31 0.1783 0.0835 -0.0646 0.1096 -0.0564 0.2835 0.0571 -0.0034 -0.0667 0.0647 -0.0398 -0.0179 -0.0988 0.0485 0.0075 0.1515 -0.0045 -0.0104 0.1806 -0.0262 0.1011 58.4441 31.4864 37.4915 32 0.0268 0.0058 -0.0097 0.016 0.0359 0.1542 0.0128 -0.0245 -0.0094 0.0402 -0.0712 0.032 -0.0775 -0.0113 -0.0063 0.1069 -0.033 0.0183 0.09 -0.0134 0.0752 52.0644 38.176 24.824 33 0.1362 -0.0707 0.0978 0.0394 -0.0506 0.0724 0.03 -0.0486 0.0594 -0.0369 0.0252 -0.0628 0.0285 0.0929 0.0013 0.0749 -0.021 0.0158 0.1875 -0.011 0.1386 63.4637 40.6507 8.6068 34 0.4166 0.1642 0.0745 0.1846 -0.1801 0.4055 -0.0378 -0.0131 -0.0252 0.0123 -0.0385 -0.0564 -0.045 0.0286 0.0194 0.126 -0.037 0.023 0.1689 -0.0476 0.1383 67.7306 48.7755 25.5073 35 0.1271 -0.1163 0.0542 0.1358 0.0187 0.2208 0.0662 0.0567 0.0246 -0.0416 -0.042 0.063 0.1225 0.1073 -0.0117 0.0841 0.0043 0.0126 0.0995 -0.0103 0.0905 57.035 29.5807 15.7679 36 0.0842 -0.0663 0.0733 0.2231 -0.1929 0.6257 -0.0029 -0.1091 0.0899 0.0881 0.0214 -0.1412 -0.26 0.0519 -0.0511 0.2029 -0.0486 0.0438 0.1702 -0.0592 0.152 60.9763 50.2789 25.0177 37 0.1922 -0.2003 -0.0245 0.3507 -0.0051 0.0103 0.0259 -0.0492 -0.0881 0.0159 -0.0184 -0.0982 0.0478 -0.0083 0.0176 0.0874 -0.0778 0.004 0.161 0.0181 0.4057 13.4836 43.0318 -4.8119 38 0.2425 -0.0023 -0.0867 0.1909 -0.1458 0.1631 0.0597 -0.1641 0.1002 0.1595 0.0431 0.2388 -0.0982 -0.0534 0.048 0.088 -0.0046 0.0503 0.0798 -0.0076 0.1554 21.1634 52.4387 -3.0887 39 0.5547 0.1981 -0.024 0.305 0.0043 0.1426 0.1054 -0.0841 0.0606 0.0361 0.0024 0.0864 0.0783 -0.0974 -0.0401 0.1231 -0.0172 0.0462 0.1641 0.0322 0.1587 25.2835 45.375 9.8445 40 0.0768 -0.0391 0.0861 0.0652 -0.1135 0.2704 -0.0866 0.0915 0.0939 0.0537 -0.0156 0.0294 -0.1458 -0.0156 -0.003 0.1091 0.065 0.0436 0.1418 0.0449 0.1831 18.8018 59.8591 -11.5664 41 0.0187 0.0251 0.0067 0.0521 0.0365 0.0493 -0.0256 0.0946 0.0611 0.0503 -0.0234 0.0884 0.0082 -0.0298 -0.0219 0.0657 0.0682 0.0942 0.1713 0.0504 0.2232 13.0814 58.1215 -7.4512 42 0.5613 -0.0059 -0.0338 0.4359 0.0436 0.2867 -0.0194 -0.0326 0.0181 0.1312 -0.0069 0.041 -0.0147 0.0522 -0.0045 0.155 -0.0087 0.0342 0.1606 -0.0297 0.1693 32.2793 51.6569 7.7325 43 0.035 -0.0414 0.0284 0.0521 -0.038 0.044 -0.0268 -0.0243 0.0223 0.0877 -0.0055 0.027 0.0277 0.0658 -0.0057 0.12 -0.02 0.0256 0.1216 -0.0155 0.0818 35.832 50.3536 2.0062 44 0.1898 0.0056 0.0011 0.0783 -0.0425 0.0289 0.128 -0.0251 0.1541 0.0709 0.0541 0.1529 -0.197 -0.0422 0.0534 0.141 0.0858 0.1637 0.149 0.0678 0.2923 12.0746 57.6161 3.0182 45 0.0481 -0.0026 -0.002 0.006 -0.0092 0.0326 0.0125 0.0096 0.0006 0.0358 0.0577 0.0332 -0.0502 0.0166 -0.0188 0.1871 -0.0092 0.072 0.1332 -0.0638 0.2689 18.0101 58.8106 16.15 46 0.0603 -0.0671 0.0245 0.0796 -0.0288 0.0091 0.0554 0.0397 0.0795 0.0809 -0.0315 0.1282 -0.0462 0.0109 -0.0931 0.1277 0.1289 0.1686 -0.1076 -0.0436 0.2419 21.3762 65.8286 -4.0507 47 0.2153 0.0291 0.0108 0.018 -0.0545 0.2118 0.0881 0.0177 0.1438 0.1025 0.0337 0.1927 -0.1704 0.0307 -0.0603 0.1495 -0.0257 0.0496 0.0851 -0.0113 0.1182 24.2416 56.5646 -3.1811 48 0.1497 -0.068 -0.0831 0.1116 0.0019 0.2054 0.0828 -0.1433 0.105 0.136 -0.0136 0.0692 0.0285 -0.0035 -0.0036 0.2411 -0.0164 0.1639 0.1989 -0.0151 0.2396 13.8378 49.4972 12.4679
Refinement TLS group Show large table (4 x 48) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 (chain A and resid 1:27)2 X-RAY DIFFRACTION 2 (chain A and resid 28:55)3 X-RAY DIFFRACTION 3 (chain A and resid 56:71)4 X-RAY DIFFRACTION 4 (chain A and resid 72:82)5 X-RAY DIFFRACTION 5 (chain A and resid 83:101)6 X-RAY DIFFRACTION 6 (chain A and resid 102:116)7 X-RAY DIFFRACTION 7 (chain A and resid 117:136)8 X-RAY DIFFRACTION 8 (chain A and resid 137:152)9 X-RAY DIFFRACTION 9 (chain A and resid 153:158)10 X-RAY DIFFRACTION 10 (chain A and resid 159:198)11 X-RAY DIFFRACTION 11 (chain A and resid 199:211)12 X-RAY DIFFRACTION 12 (chain A and resid 212:218)13 X-RAY DIFFRACTION 13 (chain B and resid 1:12)14 X-RAY DIFFRACTION 14 (chain B and resid 13:27)15 X-RAY DIFFRACTION 15 (chain B and resid 28:34)16 X-RAY DIFFRACTION 16 (chain B and resid 35:41)17 X-RAY DIFFRACTION 17 (chain B and resid 42:60)18 X-RAY DIFFRACTION 18 (chain B and