Software Name Version Classification PHENIX(phenix.refine: 1.7.3_928)refinement iMOSFLMdata reduction SCALAdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB ENTRY 2QLGResolution : 1.65→33.87 Å / SU ML : 0.25 / σ(F) : 1.34 / Phase error : 26.88 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.2268 2726 5.08 % RANDOM Rwork 0.1904 - - - obs 0.1923 53662 97.36 % -
Solvent computation Shrinkage radii : 0.86 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 32.47 Å2 / ksol : 0.356 e/Å3 Displacement parameters Baniso -1 Baniso -2 Baniso -3 1- -3.6601 Å2 -0 Å2 0 Å2 2- - -2.3107 Å2 -0 Å2 3- - - 5.9362 Å2
Refinement step Cycle : LAST / Resolution : 1.65→33.87 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 3346 0 1 408 3755
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.012 3592 X-RAY DIFFRACTION f_angle_d1.44 4884 X-RAY DIFFRACTION f_dihedral_angle_d13.241 1357 X-RAY DIFFRACTION f_chiral_restr0.086 504 X-RAY DIFFRACTION f_plane_restr0.008 643
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 (%)1.65-1.68 0.3845 150 0.325 2635 X-RAY DIFFRACTION 97 1.68-1.7123 0.3764 162 0.308 2615 X-RAY DIFFRACTION 97 1.7123-1.7473 0.348 145 0.288 2609 X-RAY DIFFRACTION 96 1.7473-1.7853 0.3511 120 0.275 2649 X-RAY DIFFRACTION 96 1.7853-1.8268 0.271 147 0.2362 2650 X-RAY DIFFRACTION 98 1.8268-1.8725 0.2988 152 0.2228 2672 X-RAY DIFFRACTION 98 1.8725-1.9231 0.2362 130 0.2021 2693 X-RAY DIFFRACTION 98 1.9231-1.9797 0.2248 146 0.1946 2641 X-RAY DIFFRACTION 98 1.9797-2.0436 0.232 149 0.1844 2675 X-RAY DIFFRACTION 97 2.0436-2.1166 0.2312 153 0.1889 2608 X-RAY DIFFRACTION 96 2.1166-2.2013 0.2239 139 0.1813 2661 X-RAY DIFFRACTION 97 2.2013-2.3015 0.2567 152 0.1739 2687 X-RAY DIFFRACTION 98 2.3015-2.4228 0.199 134 0.1689 2711 X-RAY DIFFRACTION 98 2.4228-2.5745 0.2434 136 0.1694 2715 X-RAY DIFFRACTION 98 2.5745-2.7732 0.1933 128 0.1741 2651 X-RAY DIFFRACTION 95 2.7732-3.0522 0.2013 151 0.178 2714 X-RAY DIFFRACTION 98 3.0522-3.4934 0.214 146 0.1828 2731 X-RAY DIFFRACTION 98 3.4934-4.3998 0.1852 120 0.1539 2743 X-RAY DIFFRACTION 96 4.3998-33.8767 0.2053 166 0.2047 2876 X-RAY DIFFRACTION 98
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 40) 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 0.1473 -0.0155 -0.0753 0.0463 0.0212 0.0597 0.02 0.0191 -0.0127 -0.0279 -0.0118 -0.0415 -0.0228 -0.0272 0.0421 0.1723 0.0367 0.0764 0.1835 -0.0746 0.3249 -7.9397 -24.5962 -6.0625 2 0.2245 0.0116 -0.0886 0.0088 -0.0355 0.1516 0.0749 0.1589 -0.1887 -0.0294 0.0854 -0.1154 0.2525 -0.0634 0.0025 0.1271 -0.0073 -0.0193 0.1017 -0.0116 0.2026 -11.266 -25.6737 8.2078 3 0.1001 0.2562 0.2356 0.6663 0.567 0.6919 0.0812 -0.0263 -0.2123 -0.0312 0.1497 0.001 0.0293 0.0833 0.0466 0.2499 -0.0126 -0.0688 0.1529 0.0611 0.2052 -8.5805 -20.4106 27.3351 4 0.3847 -0.0369 0.1231 0.1935 0.1062 0.3012 0.079 0.1377 -0.1541 0.0479 0.0062 -0.0426 0.0581 0.0598 0.0301 0.1052 -0.0115 -0.0097 0.1075 0.0029 0.1351 -14.1699 -19.0811 12.9087 5 0.0355 -0.016 -0.071 0.0072 0.0318 0.1417 -0.0195 0.0345 -0.0297 0.0602 -0.0492 0.0014 -0.0989 0.0212 -0.0984 0.0674 -0.026 -0.0125 0.0776 -0.0274 0.0874 -7.9084 -14.9481 0.6488 6 0.0564 0.0001 0.0247 0.0216 0.0333 0.0614 -0.0896 0.196 -0.0983 0.0553 -0.0213 -0.0073 -0.0629 -0.0549 0 0.1397 0.0008 -0.008 0.1232 -0.0336 0.1638 0.2391 -16.9301 -1.8676 7 0.2836 0.0327 -0.1589 0.4601 0.0909 0.1184 0.1031 -0.0926 -0.1343 0.0104 0.0033 -0.213 0.0397 0.0162 0.0393 0.0946 0.0193 -0.0261 0.068 -0.0097 0.1319 -2.2779 -12.9066 17.1678 8 0.216 -0.0268 -0.2564 0.0033 0.0312 0.3052 -0.0946 0.0111 -0.2628 -0.0619 0.0965 -0.0489 -0.0327 0.0632 -0.0116 0.1964 0.0138 -0.0754 0.1047 -0.0337 0.3162 -6.0944 -26.8404 8.0852 9 0.0088 -0.0199 -0.0112 0.0859 0.0421 0.021 0.0765 -0.11 -0.0713 0.0127 0.0792 -0.1528 0.0433 0.0221 0.0021 0.1789 -0.0032 -0.0159 0.2032 0.0008 0.1149 -6.467 -10.8964 28.5689 10 0.0691 0.0277 0.0323 0.0649 0.0588 0.0546 0.0227 -0.1424 0.1444 -0.0122 0.1357 0.0792 -0.0334 -0.0571 0.008 0.1844 0.0507 0.0184 0.2213 0.0032 0.1308 -16.8585 -6.8238 28.0686 11 0.0079 0.0045 0.0098 0.0055 0.0088 0.0156 -0.0114 -0.1763 -0.0572 -0.1304 0.0486 -0.0707 -0.0915 -0.1239 0.0003 0.1788 0.0123 0.0185 0.1827 0.001 0.1503 -17.3033 -4.9768 15.2601 12 0.0139 0.0163 -0.0116 0.0337 0.0099 0.0777 -0.1226 0.1405 0.0136 0.2991 0.0401 -0.1454 0.059 0.0708 -0.0001 0.1414 -0.0067 -0.044 0.1111 0.0021 0.1975 2.0255 -5.5746 6.0966 13 0.0429 0.0327 -0.0173 0.0243 -0.0128 0.006 -0.0003 0.0436 0.2068 0.1115 0.1113 -0.103 0.0771 -0.0297 0.0001 0.1458 0.0157 0.0207 0.153 -0.0063 0.1473 -8.25 -3.2275 13.3744 14 0.1501 -0.0001 0.0698 0.0389 -0.04 0.073 -0.1079 -0.1713 0.0896 -0.0225 -0.285 0.0965 -0.0626 -0.1269 -0.0074 0.2373 0.0313 0.0474 0.1708 -0.0289 0.2508 -17.1304 0.5186 21.0695 15 0.0003 -0.0022 0.0033 0.0143 -0.0215 0.0316 0.1286 0.0402 0.0768 0.0561 0.0029 -0.0905 0.0565 0.0807 -0 0.1581 0.0086 0.0097 0.1448 -0.0164 0.1528 -0.2605 -7.8461 12.8973 16 0.0063 -0.0017 -0.0004 0.004 0.003 0.0023 -0.1497 -0.0715 -0.0428 -0.0403 -0.0381 0.101 0.0672 0.0166 -0.0002 0.1219 0.0131 -0.0006 0.188 -0.0209 0.1906 7.3481 -20.8971 4.9144 17 0.0307 -0.0174 0.0374 0.0097 -0.021 0.0443 0.0536 0.0587 -0.0229 -0.0349 0.0411 0.0452 -0.073 0.0158 -0 0.1214 0.0048 -0.0098 0.1353 -0.0027 0.1521 0.6987 -8.8554 -0.0688 18 0.3479 -0.3056 -0.1835 1.2373 -0.3392 0.355 0.0303 0.0275 0.1246 -0.1579 -0.1201 -0.0762 0.0885 -0.0399 -0.0701 0.0821 -0.0007 -0.0064 0.1712 -0.0242 0.0833 -21.053 -12.6313 11.6963 19 0.011 -0.0053 0.0008 0.014 -0.0077 0.0045 -0.0124 0.0262 -0.074 -0.0062 -0.1186 0.1628 -0.0171 -0.1931 -0.0001 0.154 -0.0367 0.0254 0.1595 -0.0022 0.1767 -22.2038 -18.9868 18.3435 20 0.008 -0.0145 -0.0018 0.0274 0.0076 0.0141 0.0003 0.0345 -0.0518 0.0404 -0.0134 -0.0454 -0.0654 -0.1045 0 0.1271 0.0046 0.0065 0.1252 0.0093 0.1615 -9.9928 -7.3493 0.1827 21 0.0061 0.0199 -0.0022 0.2318 0.0527 0.0228 0.0465 0.0059 -0.0699 0.0693 -0.0922 0.0574 0.1034 0.3384 0.0005 0.1369 -0.0244 -0.029 0.1748 0.0623 0.1564 11.5487 -24.9959 53.089 22 0.1859 -0.0384 -0.0131 0.0504 0.0094 0.0734 0.0244 0.0278 -0.1037 -0.0723 0.1249 0.1641 0.0678 -0.1055 -0.0413 0.1245 -0.0035 -0.0352 0.1022 0.0293 0.0991 11.3687 -23.5304 33.5033 23 0.3843 -0.2449 -0.3183 0.4035 -0.0552 0.5325 0.073 0.0677 -0.0911 0.009 0.0893 -0.0037 0.0552 0.0093 0.1423 0.1389 -0.0203 -0.074 0.1375 -0.0665 0.2287 11.707 -22.2308 20.264 24 0.0565 0.0139 -0.0314 0.0023 -0.0039 0.1825 0.0376 -0.0983 -0.1479 0.0089 -0.0159 -0.019 0.1067 0.0246 0.0271 0.1177 0.007 -0.0062 0.1395 0.0079 0.0787 17.1533 -22.2027 39.1771 25 0.0535 -0.0246 0.021 0.0613 -0.0504 0.0408 -0.0652 -0.0466 0.0067 0.0524 0.0517 0.0643 -0.0544 0.2027 -0 0.1466 -0.0066 -0.015 0.1705 0.0344 0.1484 14.7738 -14.9967 29.844 26 0.0466 -0.0652 0.0173 0.0923 -0.0234 0.0069 -0.0292 -0.0461 -0.1288 -0.0938 -0.151 0.0423 -0.0494 0.0267 -0.0129 0.095 0.0136 -0.0125 0.1304 0.0033 0.0946 9.3897 -14.5304 48.2099 27 0.0434 0.017 -0.0287 0.0184 -0.0082 0.0732 -0.0151 -0.1011 -0.0278 -0.0296 0.073 0.0373 -0.094 -0.0149 0.004 0.1267 0.0016 0.0031 0.1208 0.0299 0.1314 1.2022 -17.6426 50.1929 28 0.1913 -0.0132 -0.1529 0.3751 -0.2751 0.596 0.0544 0.0951 0.067 -0.0436 0.0448 0.0558 -0.0863 -0.0578 0.5563 0.0806 -0.0262 -0.0284 0.0416 0.0737 0.0371 4.1164 -13.9082 31.8636 29 0.0062 0.0037 0.0114 0.0018 0.0062 0.0187 -0.0229 0.122 -0.2216 -0.0149 0.0953 -0.0153 0.0629 0.0366 -0 0.1551 -0.0024 -0.0309 0.118 0.0044 0.1717 7.7121 -26.4531 38.4693 30 0.0305 -0.0444 -0.0188 0.0642 0.0277 0.012 -0.0799 0.168 0.0262 -0.0157 0.1452 0.1345 0.0837 0.0591 0.0047 0.1667 -0.0273 -0.015 0.2342 0.0744 0.122 10.885 -8.5153 18.1627 31 0.0548 -0.0303 -0.0436 0.0166 0.024 0.0345 0.0455 0.12 0.0733 0.0046 0.0358 0.0356 -0.1465 -0.0114 0.0252 0.1518 -0.0652 0.0146 0.2685 0.0765 0.113 19.7327 -8.3502 20.5775 32 0.4677 0.0191 0.2624 0.0157 0.0199 0.1528 -0.0783 0.0714 -0.0117 0.0714 0.0418 0.029 -0.0993 0.105 -0.0309 0.1893 -0.0861 0.0137 0.1505 0.0524 0.1609 19.8751 -4.4827 32.53 33 0.0055 -0.0161 0.0076 0.0552 -0.0315 0.019 -0.13 -0.0163 0.0889 -0.112 0.1317 0.0801 -0.015 -0.0727 -0 0.1624 0.0039 0.0014 0.1128 0.0212 0.1738 0.4381 -5.7323 41.9419 34 0.0026 -0.0029 0.0021 0.003 -0.0024 0.0018 -0.0594 0.0037 0.0662 -0.0756 -0.0827 -0.0209 -0.0703 -0.0514 -0.0004 0.1153 0.0017 0.0225 0.1073 0.0069 0.2278 -0.3758 -5.8552 39.4364 35 0.227 0.1049 0.0341 0.1533 -0.1818 0.3774 0.0041 0.0634 0.1388 0.2593 -0.0081 0.0149 -0.0313 -0.0211 -0.1054 0.1624 -0.0213 0.0282 0.1241 0.0968 0.1984 15.1444 -2.1433 31.9711 36 0.0336 0.1352 0.1424 0.548 0.5755 0.6052 -0.0817 -0.0148 0.111 -0.055 -0.1272 -0.2019 -0.1445 0.2204 -0.4451 0.2053 -0.0655 -0.0128 0.1857 0.0893 0.1878 15.6323 -0.2535 28.3341 37 0.0066 -0.0073 -0.0038 0.0122 0.0106 0.0117 0.0275 0.0653 -0.0043 0.031 -0.1039 0.0479 0.1806 -0.1176 0 0.133 -0.0243 0.0079 0.1695 0.0347 0.1437 -0.7865 -11.8487 37.8493 38 0.0864 -0.0106 0.0964 0.0022 0.0035 0.1665 -0.0299 0.0868 0.0225 0.038 0.0218 0.0582 0.0082 0.0068 -0.0001 0.1148 -0.0053 0.0256 0.1333 0.0258 0.1255 8.758 -12.4514 42.7443 39 0.2861 0.0648 -0.0056 0.163 0.0405 0.0117 -0.0739 0.0357 0.0098 -0.0012 -0.0849 -0.0304 -0.1023 0.169 -0.0526 0.1574 0.0207 0.014 0.2168 0.0259 0.0716 23.8024 -19.2514 29.4636 40 0.4043 0.0651 0.2788 0.1266 0.1719 0.3325 0.0342 0.2376 0.1241 0.0177 0.0349 0.0644 -0.1184 -0.0393 0.0458 0.1677 0.015 0.0224 0.107 0.0383 0.1442 12.0268 -7.4426 47.8127
Refinement TLS group Show large table (4 x 40) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 (chain A and resid 6:10)2 X-RAY DIFFRACTION 2 (chain A and resid 11:18)3 X-RAY DIFFRACTION 3 (chain A and resid 19:28)4 X-RAY DIFFRACTION 4 (chain A and resid 29:69)5 X-RAY DIFFRACTION 5 (chain A and resid 70:74)6 X-RAY DIFFRACTION 6 (chain A and resid 75:91)7 X-RAY DIFFRACTION 7 (chain A and resid 92:113)8 X-RAY DIFFRACTION 8 (chain A and resid 114:123)9 X-RAY DIFFRACTION 9 (chain A and resid 124:131)10 X-RAY DIFFRACTION 10 (chain A and resid 132:140)11 X-RAY DIFFRACTION 11 (chain A and resid 141:144)12 X-RAY DIFFRACTION 12 (chain A and resid 145:156)13 X-RAY DIFFRACTION 13 (chain A and resid 157:167)14 X-RAY DIFFRACTION 14 (chain A and resid 168:174)15 X-RAY DIFFRACTION 15 (chain A and resid 175:181)16 X-RAY DIFFRACTION 16 (chain A and resid 182:185)17 X-RAY DIFFRACTION 17 (chain A and resid 186:197)18 X-RAY DIFFRACTION 18 (chain A and