Software Name Version Classification XDSdata reduction XSCALEdata scaling PHENIXdev_3500refinement PDB_EXTRACT3.25 data extraction PHASERphasing PARROTphasing ARP/wARPmodel building Cootmodel building
Refinement Method to determine structure : SAD / Resolution : 1.55→47.952 Å / SU ML : 0.14 / Cross valid method : THROUGHOUT / σ(F) : 1.35 / Phase error : 16.94 Rfactor Num. reflection % reflection Selection details Rfree 0.1686 1944 1.12 % 0 Rwork 0.1466 - - - obs 0.1469 173100 99.8 % -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 ÅDisplacement parameters Biso max : 81.01 Å2 / Biso mean : 23.0985 Å2 / Biso min : 8.46 Å2 Refinement step Cycle : final / Resolution : 1.55→47.952 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 7343 0 177 1527 9047 Biso mean - - 43.57 35.08 - Num. residues - - - - 1043
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 7751 X-RAY DIFFRACTION f_angle_d0.934 10565 X-RAY DIFFRACTION f_dihedral_angle_d12.666 4503 X-RAY DIFFRACTION f_chiral_restr0.06 1232 X-RAY DIFFRACTION f_plane_restr0.007 1405
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0 / Total num. of bins used : 14
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.55-1.5888 0.2194 130 0.2184 12097 12227 99 1.5888-1.6317 0.2411 98 0.1979 12219 12317 100 1.6317-1.6797 0.1947 151 0.1827 12193 12344 100 1.6797-1.734 0.2487 130 0.1781 12209 12339 100 1.734-1.7959 0.1895 163 0.1672 12142 12305 100 1.7959-1.8679 0.1982 175 0.1577 12181 12356 100 1.8679-1.9529 0.1981 98 0.1526 12275 12373 100 1.9529-2.0558 0.174 146 0.1498 12216 12362 100 2.0558-2.1846 0.1595 142 0.1443 12190 12332 100 2.1846-2.3533 0.1402 116 0.1402 12279 12395 100 2.3533-2.5901 0.1851 142 0.1493 12232 12374 100 2.5901-2.9649 0.1587 136 0.1439 12240 12376 100 2.9649-3.7352 0.1638 151 0.1342 12290 12441 100 3.7352-47.9745 0.14 166 0.1271 12393 12559 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 15) 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 2.0127 0.153 -0.9914 0.4747 -0.3854 1.4316 -0.0098 -0.0367 0.0944 -0.0235 -0.0024 -0.0192 -0.1268 0.0541 0.0279 0.1434 -0.0105 -0.006 0.2002 0.0298 0.1347 0.6589 40.6064 -35.6988 2 0.3972 -0.2336 -0.3528 0.8078 -0.3401 0.7531 -0.0071 0.3127 -0.278 -0.0427 0.0352 0.202 0.064 -0.3173 0.0503 0.13 -0.02 0.0043 0.3386 -0.0282 0.2142 -19.8879 27.2554 -44.6872 3 0.6985 0.4201 -0.2605 1.2258 -0.3856 0.8182 -0.0385 0.5398 -0.3373 -0.0786 0.0464 0.1799 0.1674 -0.3138 0.0277 0.169 -0.0538 0.0156 0.3949 -0.0898 0.3444 -27.7605 23.125 -45.8735 4 0.1725 -0.2302 0.0565 0.3086 -0.2049 1.3327 -0.0018 -0.0253 0.0188 -0.0729 -0.0161 0.0308 0.0268 -0.0079 0.0758 0.1004 0.0068 -0.0119 0.1214 0.0083 0.1164 -4.9546 39.6434 -58.0998 5 0.2989 -0.0978 0.1899 0.3075 -0.3917 0.5224 -0.0231 -0.0802 0.0219 -0.0114 0.017 -0.0256 -0.1072 -0.0654 0.0097 0.1491 0.0104 -0.0098 0.1073 0.0093 0.1319 -10.5522 54.2689 -70.7458 6 0.7096 -0.035 -0.0087 0.4077 -0.1748 0.943 -0.0066 -0.0334 -0.0013 -0.0422 0.0387 0.0048 0.0569 -0.0649 -0.0339 0.1395 -0.0004 -0.0161 0.1129 0.0079 0.1402 -13.9706 45.7681 -79.4931 7 0.053 -0.1052 0.028 0.3003 -0.4674 1.446 -0.0309 -0.0383 0.0206 0.0307 0.0934 0.0526 -0.1746 -0.2567 -0.0679 0.1506 0.0303 -0.0031 0.1984 0.0122 0.1539 -14.5737 49.1717 -58.9187 8 0.4344 0.0247 0.0941 0.4685 -0.1378 1.0444 0.0024 -0.0176 -0.0324 -0.0137 -0.0134 -0.0182 -0.0029 0.0038 0.0082 0.1302 0.0095 -0.0063 0.1698 0.0197 0.1389 -3.775 37.74 -49.6398 9 0.7853 0.7883 -0.1419 0.9148 -0.3829 0.883 -0.0309 0.1126 0.1915 -0.0257 0.0245 0.1184 -0.1386 -0.1654 0.0067 0.1562 0.0203 -0.0024 0.2153 0.0264 0.1616 5.9423 40.5436 -28.0354 10 1.6153 -0.1233 -0.5304 0.2309 0.0234 0.5766 0.0629 -0.0481 0.0048 0.0005 -0.0559 -0.0593 -0.014 0.0988 -0.0068 0.1272 -0.013 0.0168 0.1614 0.0292 0.1472 33.8355 32.694 -24.3095 11 0.3506 -0.1104 0.1262 0.6956 0.122 1.0242 0.0219 -0.0085 0.0097 0.0695 -0.0325 0.0634 0.0553 -0.1438 0.0038 0.1233 -0.0199 0.0097 0.1202 -0.0078 0.1342 9.9965 30.677 -3.161 12 0.839 -0.1408 0.2557 0.4429 -0.1272 1.3519 -0.0284 -0.1547 0.0707 0.0937 0.0097 0.0608 -0.0868 -0.129 0.0136 0.1465 -0.014 0.0104 0.1469 -0.0195 0.1395 14.8551 38.592 10.4634 13 0.8953 0.047 0.107 0.5987 -0.0402 1.7311 -0.0041 -0.1769 -0.0549 0.0568 0.0011 -0.0127 0.1498 -0.0215 0.0004 0.1415 -0.0082 -0.0098 0.1357 0.0091 0.1263 22.5535 29.2048 14.0245 14 0.6511 -0.1496 0.0336 0.3656 -0.105 1.0721 0.0192 -0.1345 0.0747 0.055 0.0247 0.0358 -0.1099 -0.1142 -0.0271 0.1523 -0.0076 0.002 0.1303 -0.0114 0.1567 13.3511 42.5408 4.6206 15 1.0649 -0.0247 0.0409 0.4737 0.1417 0.8798 0.0073 0.0587 0.0515 -0.0016 -0.0118 -0.0209 -0.0384 0.0181 0.0028 0.1101 -0.0091 0.0031 0.1011 0.0121 0.113 17.6879 36.2436 -14.8161
Refinement TLS group ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 40 through 67 )A40 - 67 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 68 through 108 )A68 - 108 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 109 through 153 )A109 - 153 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 154 through 272 )A154 - 272 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 273 through 306 )A273 - 306 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 307 through 401 )A307 - 401 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 402 through 486 )A402 - 486 8 X-RAY DIFFRACTION 8 chain 'A' and (resid 487 through 562 )A487 - 562 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 40 through 67 )B40 - 67 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 68 through 183 )B68 - 183 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 184 through 272 )B184 - 272 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 273 through 306 )B273 - 306 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 307 through 401 )B