Software Name Version Classification NB SCALEPACKdata scalingShow PHASER2.1.4phasingShow PHENIX1.7.3_928refinementShow PDB_EXTRACT3.11 data extractionShow Blu-Icedata collection DENZOdata reduction
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.085→19.761 Å / Occupancy max : 1 / Occupancy min : 0.92 / SU ML : 0.23 / σ(F) : 0 / Phase error : 23.63 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.2273 1928 5.02 % random Rwork 0.1895 - - - all 0.1915 38376 - - obs 0.1915 38376 96.87 % -
Solvent computation Shrinkage radii : 0.86 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 41.147 Å2 / ksol : 0.366 e/Å3 Displacement parameters Biso max : 113.5 Å2 / Biso mean : 37.6615 Å2 / Biso min : 9.74 Å2 Baniso -1 Baniso -2 Baniso -3 1- -3.241 Å2 -0 Å2 0.6383 Å2 2- - -4.2759 Å2 0 Å2 3- - - -3.2925 Å2
Refinement step Cycle : LAST / Resolution : 2.085→19.761 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 5024 0 6 245 5275
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.009 5140 X-RAY DIFFRACTION f_angle_d1.162 6952 X-RAY DIFFRACTION f_chiral_restr0.081 752 X-RAY DIFFRACTION f_plane_restr0.007 912 X-RAY DIFFRACTION f_dihedral_angle_d14.93 1906
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Type Rms dev position (Å)1 1 A2333 X-RAY DIFFRACTION POSITIONAL0.014 1 2 B2333 X-RAY DIFFRACTION POSITIONAL0.014
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 14
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.0847-2.1368 0.2577 111 0.2163 2177 2288 80 2.1368-2.1945 0.2412 128 0.2019 2423 2551 92 2.1945-2.2589 0.2552 149 0.2026 2626 2775 97 2.2589-2.3318 0.2973 121 0.2007 2608 2729 98 2.3318-2.415 0.2529 124 0.1823 2648 2772 99 2.415-2.5115 0.2167 147 0.1806 2642 2789 99 2.5115-2.6255 0.2141 137 0.1836 2679 2816 99 2.6255-2.7636 0.2605 121 0.2 2679 2800 99 2.7636-2.9362 0.2833 144 0.2185 2674 2818 100 2.9362-3.1621 0.2304 162 0.2002 2645 2807 99 3.1621-3.4787 0.2259 147 0.1916 2670 2817 100 3.4787-3.9785 0.2012 143 0.1788 2685 2828 100 3.9785-4.9991 0.1733 149 0.1613 2671 2820 100 4.9991-19.7615 0.2422 145 0.1964 2621 2766 96
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 0.5164 -0.2514 -0.1008 3.273 0.6124 2.0766 -0.0746 -0.2169 -0.0505 0.4935 0.0172 -0.2358 0.039 0.291 0.0446 0.2217 0.0242 -0.0058 0.5264 0.1631 0.1791 16.6222 25.2384 22.2459 2 0.7956 -0.4039 0.6706 0.8189 -0.5757 1.4136 -0.0532 -0.1397 -0.1946 0.0914 -0.005 -0.0392 0.0461 0.0263 -0.2572 0.2245 0.0356 0.0288 0.0814 0.1118 0.1982 6.3382 23.8499 -0.6499 3 7.8354 0.1566 -1.4892 6.1204 -4.9329 4.9128 0.0371 0.0601 -0.1768 -0.0509 0.0468 0.4007 0.3236 -0.3849 -0.0892 0.2773 -0.1491 0.1038 0.3452 0.0742 0.4255 -4.2987 20.8298 4.5799 4 1.0255 -1.1516 0.6336 1.8629 -1.0575 1.2616 0.0255 -0.1302 -0.201 -0.0088 0.0489 0.1308 0.135 -0.0809 -0.1401 0.4297 -0.0855 0.0759 0.264 0.1961 0.4324 5.4847 12.0961 12.4102 5 0.6244 0.2938 -0.3313 0.711 -0.1908 0.5457 -0.0762 -0.2049 -0.2096 -0.0013 -0.0036 -0.0556 0.1 0.0934 -0.1003 0.1713 0.0454 0.0256 0.162 0.1075 0.1263 10.1585 25.0381 8.7553 6 2.4195 -1.147 -1.606 7.4685 -0.9561 5.3185 -0.1095 0.0492 -0.1705 0.0936 0.1441 0.3815 0.2266 -0.5434 -0.0106 0.2159 -0.0006 0.1307 0.4167 0.105 0.2583 1.7933 22.8601 16.8654 7 1.0972 -0.1527 0.2032 1.3705 0.001 0.6753 0.015 -0.0285 -0.0798 -0.1215 -0.0636 -0.1195 0.2733 0.0622 0.0933 0.1425 0.0284 0.0478 0.2093 0.0858 0.1662 12.9056 30.5264 4.2217 8 2.6179 -2.0996 -1.6587 2.6826 0.1894 2.3543 0.0582 0.4122 0.0377 -0.3981 -0.0953 -0.2068 0.007 0.282 0.0198 0.5112 -0.1369 0.0433 0.413 0.0252 0.464 15.5742 46.743 -7.4214 9 2.2052 0.6195 -0.7972 1.9614 -0.4189 2.4351 -0.0322 -0.102 0.2471 0.0745 0.027 -0.0576 -0.2639 0.1064 0.0105 0.1223 -0.0473 0.0299 0.1978 -0.0666 0.1842 17.3217 43.2676 5.7902 10 2.1989 -0.1919 -1.1944 0.3588 -0.1456 0.8301 0.0455 -0.1878 -0.0198 0.0413 -0.0338 -0.02 -0.0577 -0.0517 0.0179 0.0707 0.0282 0.0101 0.305 0.0234 0.0971 13.833 33.5746 8.9778 11 3.8139 -2.7345 -0.5709 2.9253 1.9033 3.3434 0.0742 0.3402 0.1387 -0.8033 0.0732 -0.3815 -0.2579 0.1664 -0.0973 0.2801 0.0981 0.0233 0.3458 0.0285 0.2239 26.7901 32.5681 -9.645 12 2.5147 0.3534 -0.2081 1.0166 -0.5269 1.3206 0.0032 -0.2553 0.1513 0.0954 -0.0712 -0.0195 -0.1097 0.1209 0.0554 0.0496 -0.0285 -0.0182 0.2691 -0.0405 0.1535 24.3532 37.7571 5.0701 13 1.1713 0.4155 0.1981 0.6633 0.1997 1.0515 0.0293 -0.0502 -0.3338 0.0063 -0.0348 -0.076 0.1569 0.2355 -0.1474 0.0831 0.1039 -0.0215 0.3171 0.0685 0.2674 30.2857 25.2705 0.6901 14 0.9425 0.1204 0.0241 1.164 0.5641 0.368 -0.0157 0.1246 -0.0205 -0.1003 -0.1439 0.1766 0.0375 0.1445 -0.1016 0.1772 0.122 0.0215 0.2973 0.1507 0.3724 26.3396 17.6909 0.255 15 2.0318 0.2637 1.9386 2.1456 -0.0933 1.9061 0.0834 0.1162 -0.2819 -0.0516 0.014 -0.1285 0.2739 0.2262 -0.0941 0.4671 0.1674 0.1767 0.2924 0.0419 0.6754 27.2618 7.3157 -2.4439 16 0.5641 -0.3053 0.076 0.6819 0.235 0.1578 0.0914 0.0102 -0.1239 0.0719 0.0252 -0.0967 0.1789 0.0942 -0.0563 0.3323 0.1898 -0.0216 0.4314 0.2024 0.5009 34.1529 12.9004 8.3573 17 1.9765 -0.4666 0.5491 0.3559 -0.4506 0.5722 -0.0658 0.117 -0.4598 -0.2257 -0.0272 -0.088 0.2824 0.1421 -0.0405 0.3844 -0.0028 0.075 0.1148 0.0258 0.4507 8.2129 15.1552 -4.0986 18 0.3997 -0.3676 0.2437 1.3492 -0.4291 0.4649 0.0809 -0.0228 -0.1803 -0.066 -0.0394 0.0238 0.2794 0.0382 -0.0855 0.4916 0.0241 0.0578 0.15 0.0808 0.6076 16.4246 6.0114 2.8968 19 0.9792 -0.9515 -0.7168 4.6791 2.4961 1.4862 0.0027 -0.1016 -0.1329 0.1378 0.0356 0.0659 0.1324 -0.0061 -0.0687 0.605 0.226 -0.1213 0.4654 0.2119 0.6922 30.169 2.3379 13.3328 20 0.6473 -0.3919 0.3468 1.0203 -0.1724 0.9413 0.0149 -0.0727 -0.1008 0.2094 0.0304 -0.1042 0.2154 0.0848 -0.0649 0.2586 0.108 0.0074 0.5079 0.2579 0.3517 26.2156 17.1586 16.6177 21 2.1916 0.7029 0.0093 3.5167 -0.1626 0.6157 0.0474 0.3103 0.0226 -0.3086 0.0285 0.5087 -0.0428 -0.2066 -0.0683 0.1896 0.1585 -0.0189 0.506 0.0419 0.2424 -20.4671 43.0504 -18.8078 22 1.3459 -0.635 0.882 0.7368 -0.5047 1.124 0.0199 -0.0341 0.0392 -0.0373 0.0733 0.1006 -0.1798 -0.1767 0.1257 0.1812 0.1004 0.0226 0.0812 0.0555 0.2165 1.2732 44.4473 -6.2682 23 5.1301 -5.0813 -1.8705 6.2642 -0.2962 7.3437 -0.1126 -0.3994 0.2989 0.4174 0.0557 -0.0238 -0.1886 0.0078 0.0483 0.385 0.0778 0.1165 0.3342 -0.1314 0.277 -5.0034 47.4707 3.7833 24 1.1778 -0.9704 0.6537 1.8979 -1.2988 1.193 -0.083 -0.0855 0.1237 0.1395 0.0523 0.0119 -0.2157 -0.1385 0.0037 0.4154 0.1969 0.0634 0.254 -0.0691 0.4084 -11.8048 56.1974 -6.74 25 0.5726 -0.2312 -0.2266 1.1095 0.2397 0.4556 0.0383 0.0611 0.128 -0.0257 0.0503 0.0138 -0.2141 -0.2216 -0.0033 0.1375 0.1025 0.0259 0.1686 0.0514 0.1964 -7.6973 43.2557 -11.0167 26 5.2417 -0.4085 -1.268 7.1909 -1.8269 2.1194 -0.0457 -0.5629 0.2774 0.3776 0.1451 0.0896 -0.1727 -0.0005 -0.1153 0.2152 0.1047 0.1112 0.4168 -0.0225 0.2509 -16.6138 45.4345 -3.5153 27 0.7185 0.025 0.2063 1.534 -0.0443 1.0215 0.0444 0.0865 0.2601 -0.0895 -0.0852 -0.0899 -0.0664 -0.0568 0.0134 0.1434 0.0805 0.0539 0.2157 0.042 0.1394 -2.9123 37.7796 -13.2946 28 2.4061 0.1811 -2.9454 2.6364 -2.7237 9.7176 -0.0042 0.2341 -0.0116 -0.1816 -0.0841 -0.421 0.0346 0.4397 0.0833 0.4677 0.0328 0.065 0.4267 -0.0913 0.5306 8.9464 21.5529 -14.7635 29 2.5532 -0.4009 -0.7387 1.9625 0.6261 2.1853 0.0226 0.1058 -0.2417 -0.0922 0.0612 0.0607 0.27 -0.0844 -0.0559 0.1774 -0.0608 0.0309 0.2022 -0.0456 0.1344 -4.0194 25.0259 -17.8395 30 1.0287 -0.1609 -1.2816 0.3229 -0.0671 1.8344 -0.0226 -0.032 -0.0763 -0.0026 -0.0732 0.0405 -0.0023 -0.1631 0.0005 0.0889 0.0191 0.0106 0.3186 0.016 0.0736 -7.5431 34.7175 -14.6885 31 3.196 1.8142 -0.6647 9.058 -3.2147 3.3446 -0.1171 0.1493 -0.2925 -0.2883 0.046 -0.8604 0.112 0.3746 0.0109 0.1953 0.0116 0.0361 0.3326 0.0851 0.2597 12.2875 35.7251 -25.7072 32 2.8625 -0.8547 -0.2679 1.8873 0.2845 2.7776 0.0362 0.1758 -0.2025 -0.0521 -0.0808 0.1097 0.1521 -0.2306 -0.0208 0.1797 -0.0304 -0.0014 0.2702 -0.0359 0.0502 -2.5948 30.5344 -24.7603 33 1.0491 0.0508 0.1638 1.1312 0.1234 1.5796 0.0371 0.2611 0.1705 -0.0654 -0.0392 -0.0284 -0.3659 -0.0235 0.0729 0.2538 0.0668 0.01 0.3175 0.1138 0.0826 2.3566 43.0178 -30.2289 34 0.2482 0.5568 0.0271 1.5561 0.514 1.2329 0.0786 0.0997 0.0653 0.2341 -0.012 -0.0104 -0.0134 0.1307 0.1344 0.3645 0.1326 0.0356 0.2794 0.1294 0.1815 2.3927 50.5878 -26.2614 35 1.4781 -0.1731 1.7776 1.9868 0.1843 2.216 -0.0842 0.2123 0.2527 -0.1186 0.0158 -0.0539 -0.2991 0.1304 0.0871 0.5645 0.0022 0.1393 0.266 0.1686 0.4259 5.1702 60.9743 -26.9095 36 0.1449 0.2649 0.0283 0.7346 -0.3338 0.5993 -0.0916 0.0952 0.1372 -0.1089 0.0027 0.0375 -0.148 0.0246 0.0442 0.4473 0.1779 0.0073 0.4049 0.2129 0.3048 -4.8806 55.385 -34.8536 37 0.5088 -0.493 0.3838 0.4777 -0.3634 1.7014 0.0085 0.0885 0.251 -0.0215 0.0335 -0.2924 -0.4392 0.0791 0.0172 0.3936 0.0292 0.0608 0.0891 0.0063 0.3613 4.9005 53.1467 -7.7878 38 0.3775 -0.3934 0.2492 1.4114 -0.4027 0.4396 -0.0898 0.0276 0.2894 0.0388 -0.0462 -0.0539 -0.1745 -0.0157 0.1051 0.5479 0.0752 0.0548 0.1373 0.0349 0.4698 -1.213 62.2596 -16.6497 39 1.0403 2.0108 -0.6437 4.6113 -0.7553 0.7282 -0.0679 -0.0084 0.1366 0.0057 0.0508 0.1417 -0.1342 -0.0953 0.0344 0.6645 0.1627 -0.0837 0.4175 0.2327 0.5261 -10.2341 65.948 -31.3942 40 0.8566 -0.104 0.3665 1.0016 -0.3139 0.6275 -0.0743 0.0886 0.2282 -0.0976 0.0188 0.1631 -0.1232 -0.0607 0.0615 0.3197 0.2421 0.0059 0.5115 0.1232 0.2425 -13.8985 51.127 -27.7873
Refinement TLS group Show large table (6 x 40) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 (chain A and resid 3:19)A3 - 19 2 X-RAY DIFFRACTION 2 (chain A and resid 20:41)A20 - 41 3 X-RAY DIFFRACTION 3 (chain A and resid 42:47)A42 - 47 4 X-RAY DIFFRACTION 4 (chain A and resid 48:61)A48 - 61 5 X-RAY DIFFRACTION 5 (chain A and resid 62:81)A62 - 81 6 X-RAY DIFFRACTION 6 (chain A and resid 82:87)A82 - 87 7 X-RAY DIFFRACTION 7 (chain A and resid 88:109)A88 - 109 8 X-RAY DIFFRACTION 8 (chain A and resid 110:114)A110 - 114 9 X-RAY DIFFRACTION 9 (chain A and resid 115:131)A115 - 131 10 X-RAY DIFFRACTION 10 (chain A and resid 132:149)A132 - 149 11 X-RAY DIFFRACTION 11 (chain A and resid 150:155)A150 - 155 12 X-RAY DIFFRACTION 12 (chain A and resid 156:175)A156 - 175 13 X-RAY DIFFRACTION 13 (chain A and resid 176:217)A176 - 217 14 X-RAY DIFFRACTION 14 (chain A and resid 218:240)A218 - 240 15 X-RAY DIFFRACTION 15 (chain A and