Software Name Version Classification NB XSCALEdata scalingShow PHASER2.1.4phasingShow PHENIX1.7_650refinementShow PDB_EXTRACT3.1 data extractionShow
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 3.25→29.802 Å / Occupancy max : 1 / Occupancy min : 0 / SU ML : 0.45 / σ(F) : 1.99 / Phase error : 30.39 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2969 3841 9.93 % Rwork 0.2494 - - obs 0.2542 38678 86 %
Solvent computation Shrinkage radii : 0.38 Å / VDW probe radii : 0.7 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 88.989 Å2 / ksol : 0.295 e/Å3 Displacement parameters Biso max : 499.43 Å2 / Biso mean : 118.5717 Å2 / Biso min : 8.22 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.6595 Å2 0 Å2 -0 Å2 2- - 1.9216 Å2 0 Å2 3- - - -1.2622 Å2
Refinement step Cycle : LAST / Resolution : 3.25→29.802 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 11671 0 60 32 11763
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.003 12042 X-RAY DIFFRACTION f_angle_d0.704 16399 X-RAY DIFFRACTION f_chiral_restr0.048 1902 X-RAY DIFFRACTION f_plane_restr0.003 2017 X-RAY DIFFRACTION f_dihedral_angle_d13.889 4048
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 27
Show large table (7 x 27) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)3.2501-3.2911 0.3549 10 0.3159 174 184 11 3.2911-3.3344 0.3773 25 0.2731 289 314 20 3.3344-3.38 0.3013 49 0.3147 415 464 28 3.38-3.4282 0.3395 59 0.3398 584 643 39 3.4282-3.4793 0.3456 82 0.3177 828 910 55 3.4793-3.5336 0.3576 126 0.3028 1153 1279 78 3.5336-3.5915 0.3578 158 0.2874 1396 1554 95 3.5915-3.6533 0.3549 165 0.2958 1491 1656 100 3.6533-3.7196 0.2897 164 0.2828 1473 1637 100 3.7196-3.791 0.316 167 0.258 1502 1669 100 3.791-3.8682 0.3363 162 0.2498 1455 1617 100 3.8682-3.9521 0.2866 166 0.2518 1496 1662 100 3.9521-4.0439 0.2812 165 0.2469 1492 1657 100 4.0439-4.1447 0.3002 164 0.2553 1467 1631 100 4.1447-4.2565 0.2766 167 0.2306 1505 1672 100 4.2565-4.3814 0.2908 164 0.2337 1480 1644 100 4.3814-4.5223 0.2875 167 0.2339 1505 1672 100 4.5223-4.6833 0.2765 165 0.2311 1481 1646 100 4.6833-4.8701 0.2718 168 0.2356 1517 1685 100 4.8701-5.0907 0.2855 167 0.2619 1495 1662 100 5.0907-5.3576 0.3727 167 0.2737 1510 1677 100 5.3576-5.6911 0.3405 166 0.2733 1491 1657 100 5.6911-6.127 0.3192 169 0.2624 1523 1692 100 6.127-6.7372 0.3239 169 0.2572 1516 1685 100 6.7372-7.6973 0.3115 170 0.2234 1540 1710 100 7.6973-9.643 0.1943 173 0.1708 1555 1728 100 9.643-29.8027 0.2934 167 0.265 1504 1671 92
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 20) 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 0.1374 0.0222 0.0786 0.0107 0.0088 0.0389 -0.0362 0.2008 0.0399 -0.3495 0.0012 0.1592 -0.0478 -0.0967 -0.1469 0.588 0.0413 -0.6272 0.1269 -0.0274 0.1319 -17.422 -9.2198 13.1332 2 0.0597 -0.0242 0.0001 0.0078 -0.0017 0.0548 0.019 0.1544 -0.0114 -0.1399 -0.0851 0.0713 0.0063 -0.0736 -0.1313 0.9021 0.1112 -0.9179 0.3958 -0.187 0.5026 -17.5028 -12.8175 16.3873 3 0.1408 -0.1217 0.1071 0.3496 -0.0928 0.0781 0.0993 -0.1639 -0.0393 0.0063 -0.1139 -0.0076 -0.0146 -0.1195 -0.0071 0.8727 -0.0274 -0.4296 0.8714 -0.1213 1.0557 -37.7013 -20.8822 9.017 4 0.1772 0.0725 -0.0264 0.0282 -0.021 0.1465 -0.0148 0.3605 -0.1284 -0.4182 0.0611 0.284 0.196 -0.2236 0.014 0.9414 0.0613 -0.8384 0.4068 -0.168 0.531 -22.4023 -17.0707 16.939 5 0.0552 0.0071 -0.0167 0.0901 0.0013 0.122 -0.0353 -0.0688 0.0044 0.0804 -0.0257 0.0218 0.0348 0.0257 0.0127 0.6619 -0.018 -0.0479 0.4163 0.1788 0.3647 -0.0852 19.0534 55.9501 6 0.1729 -0.0405 0.0219 0.1936 0.0375 0.0373 -0.022 0.0573 0.1595 0.1482 -0.0112 -0.0638 -0.015 0.0202 -0.0777 0.0567 0.2244 0.123 0.5314 -0.1898 0.8337 -31.1046 -24.9617 59.2762 7 0.0535 -0.0018 -0.0835 0.0066 0.001 0.0643 0.0696 -0.0527 0.0866 0.1557 0.0723 0.1494 0.0115 -0.1523 0.1687 0.3308 0.1088 0.2579 0.0914 -0.1396 0.4623 -25.6591 -28.5465 58.8421 8 0.0257 0.0116 0.0191 0.0032 0.0072 0.0336 -0.0235 -0.0134 -0.0019 -0.0346 -0.0772 0.0586 -0.1208 -0.0848 -0.0083 1.102 -0.0501 0.5456 0.8763 -0.0358 0.8635 -24.5651 -34.7748 78.9085 9 0.0758 0.0958 0.0701 0.3666 -0.0137 0.2066 -0.1612 -0.3232 0.0898 0.4581 -0.0253 0.5771 -0.0529 -0.2951 -0.1921 0.3343 0.1593 0.4619 0.2214 -0.2981 0.1149 -20.7641 -31.0202 61.2268 10 0.0089 0.0064 -0.0053 0.006 -0.004 0.0029 -0.0111 -0.0024 0.0031 -0.0044 0.0223 -0.0101 -0.0132 0.037 -0.008 1.3015 0.2064 0.012 1.281 -0.0595 1.1047 -31.9429 6.4559 48.7604 11 0.1465 -0.0777 0.0082 0.069 -0.0699 0.1088 -0.0645 0.09 -0.0028 0.0756 -0.2204 -0.4145 0.0017 0.2866 -0.1848 0.0223 -0.0603 0.0246 0.4297 0.1236 0.3941 24.49 -22.8441 55.61 12 0.245 0.1252 0.0844 0.6598 -0.016 0.2321 -0.0719 -0.0742 -0.0314 -0.2033 -0.2831 -0.4088 0.1081 0.3032 -0.3078 0.3065 0.0184 0.1097 0.1151 0.0682 0.2618 8.9432 -10.9355 41.73 13 0.0149 0.0508 -0.0661 0.2088 -0.2204 0.3516 -0.1118 0.1875 -0.1037 -0.3656 -0.3991 -0.5826 0.0537 0.3147 -0.7081 0.1395 0.2473 0.4058 0.439 0.1843 0.5947 19.3569 -18.4776 38.6556 14 0.2333 -0.0291 0.1114 0.3256 -0.1114 0.1937 -0.0301 0.332 -0.2745 -0.4854 -0.157 -0.8852 0.2619 0.5071 -0.2767 -0.0842 -0.1087 0.33 0.2547 0.1083 0.6468 19.2453 -14.725 39.8761 15 0.0565 -0.0265 0.0052 0.0159 0.008 0.1196 -0.0482 0.0227 -0.0008 -0.0016 -0.1174 -0.1407 0.004 0.2073 0.0839 0.3466 -0.1461 0.1745 0.634 -0.0894 0.898 -15.3849 9.7465 57.8998 16 0.0321 -0.0156 0.0297 0.025 -0.0053 -0.0002 0.0092 -0.1351 -0.0177 -0.0223 0.0107 -0.0579 0.0699 0.029 0.0175 0.0615 0.1481 -0.0969 0.211 0.0908 0.209 -3.0741 -27.4507 44.1857 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.3311 0.0356 -0.0594 1.3495 0.0723 1.3465 -17.7552 -35.1353 34.2713 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.7229 0.0366 0.0503 0.7116 -0.0019 0.7401 1.093 9.5561 49.3867 19 1.0637 -0.6162 -0.1309 1.092 0.9653 1.0908 -0.0287 0.0189 0.3658 -0.0217 -0.0343 -0.0249 -0.2786 0.0128 0.0277 0.5373 -0.1106 -0.1102 0.2471 -0.0483 0.3414 -9.0284 -2.9693 38.3912 20 6.998 7.0414 1.5318 7.2531 0.8897 2.863 0.1968 -2.9408 6.4941 2.284 -1.1469 1.401 -1.0074 -1.7645 0.9524 1.4233 0.1135 0.0096 1.4501 0.1278 1.089 18.6742 -11.8331 38.2868
Refinement TLS group Show large table (6 x 22) 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 57:154 )A57 - 154 2 X-RAY DIFFRACTION 2 ( CHAIN A AND RESID 155:259 )A155 - 259 3 X-RAY DIFFRACTION 3 ( CHAIN A AND RESID 260:325 )A260 - 325 4 X-RAY DIFFRACTION 4 ( CHAIN A AND RESID 326:553 )A326 - 553 5 X-RAY DIFFRACTION 5 ( CHAIN A AND RESID 554:583 )A554 - 583 6 X-RAY DIFFRACTION 6 ( CHAIN B AND RESID 57:151 )B57 - 151 7 X-RAY DIFFRACTION 7 ( CHAIN B AND RESID 152:271 )B152 - 271 8 X-RAY DIFFRACTION 8 ( CHAIN B AND RESID 272:311 )B272 - 311 9 X-RAY DIFFRACTION 9 ( CHAIN B AND RESID 312:546 )B312 - 546 10 X-RAY DIFFRACTION 10 ( CHAIN B AND RESID 547:558 )B547 - 558 11 X-RAY DIFFRACTION 11 ( CHAIN C AND RESID 57:109 )C57 - 109 12 X-RAY DIFFRACTION 12 ( CHAIN C AND RESID 110:223 )C110 - 223 13 X-RAY DIFFRACTION 13 ( CHAIN C AND RESID 224:373 )C224 - 373 14 X-RAY DIFFRACTION 14 ( CHAIN C AND RESID 374:548 )C374 - 548 15 X-RAY DIFFRACTION 15 ( CHAIN C AND