Software Name Version Classification PHENIX(1.20.1_4487: ???)refinement Aimlessdata scaling PHASERphasing XDSdata reduction
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.2→49.22 Å / SU ML : 0.19 / Cross valid method : FREE R-VALUE / σ(F) : 1.35 / Phase error : 20.89 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.21 1995 0.6 % Rwork 0.1821 - - obs 0.1823 330393 98.73 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 2.2→49.22 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 30044 0 269 2128 32441
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.002 30977 X-RAY DIFFRACTION f_angle_d0.502 42319 X-RAY DIFFRACTION f_dihedral_angle_d8.672 4607 X-RAY DIFFRACTION f_chiral_restr0.045 4907 X-RAY DIFFRACTION f_plane_restr0.003 5568
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.2-2.25 0.2903 140 0.2664 22694 X-RAY DIFFRACTION 96 2.25-2.31 0.2596 145 0.2343 23377 X-RAY DIFFRACTION 99 2.31-2.38 0.2676 143 0.226 23404 X-RAY DIFFRACTION 99 2.38-2.46 0.2518 139 0.2149 23432 X-RAY DIFFRACTION 99 2.46-2.55 0.2779 146 0.2118 23515 X-RAY DIFFRACTION 99 2.55-2.65 0.2277 138 0.2049 23480 X-RAY DIFFRACTION 99 2.65-2.77 0.227 148 0.2041 23514 X-RAY DIFFRACTION 99 2.77-2.91 0.2345 145 0.1961 23536 X-RAY DIFFRACTION 99 2.91-3.1 0.2006 134 0.1919 23304 X-RAY DIFFRACTION 98 3.1-3.34 0.2389 141 0.1939 23579 X-RAY DIFFRACTION 99 3.34-3.67 0.1962 149 0.1751 23587 X-RAY DIFFRACTION 99 3.67-4.2 0.1824 139 0.156 23551 X-RAY DIFFRACTION 99 4.2-5.29 0.1753 142 0.1374 23722 X-RAY DIFFRACTION 99 5.29-49.22 0.1762 146 0.1725 23703 X-RAY DIFFRACTION 98
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 47) 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 1.0572 0.1536 0.5759 0.643 0.2224 0.8599 0.0593 0.074 -0.2898 -0.0967 0.0022 0.0453 0.0683 0.029 -0 0.2672 -0.0119 -0.0224 0.2387 0.0214 0.3655 -84.8898 -29.4612 266.9361 2 0.943 0.1823 -0.2913 0.4771 -0.1047 0.3902 -0.0039 0.0713 -0.002 -0.1105 -0.0025 0.0762 0.0119 -0.0659 -0 0.2381 0.0045 -0.0357 0.209 0.0232 0.2539 -70.5788 -11.5613 263.7095 3 1.4506 -0.1533 0.2965 0.7262 0.298 0.0473 0.1438 0.1049 -0.0087 -0.075 -0.1557 0.1519 0.0595 -0.1266 0.0002 0.3077 -0.0088 -0.0747 0.257 0.0443 0.2995 -85.1527 -14.3363 263.2254 4 1.2345 0.2731 -0.2144 0.6018 0.4231 0.44 0.0913 -0.4519 -0.008 0.1917 -0.0929 0.1701 0.0574 -0.2086 0.0002 0.5092 0.0065 0.0986 0.5791 -0.0892 0.4406 -55.0609 4.1294 158.0471 5 1.0095 -0.1276 -0.0201 0.6252 -0.054 0.7165 -0.0655 -0.0967 0.0911 0.1186 -0.0052 0.13 -0.0633 -0.2298 -0 0.3867 0.0106 0.0489 0.3481 -0.0783 0.3696 -46.534 6.5567 145.4105 6 1.0596 -0.1412 -0.2929 1.4197 0.1596 0.3143 0.0341 -0.0893 -0.2397 0.1787 -0.008 0.101 0.2253 0.0092 -0 0.4553 -0.0232 0.0723 0.2948 -0.04 0.3261 -37.9255 -17.5791 142.5532 7 1.1833 0.1703 -0.2372 0.218 0.2453 0.2535 0.1201 -0.1413 -0.1835 0.0997 -0.1476 0.0988 -0.0083 -0.1582 0 0.4335 -0.078 0.0831 0.4326 -0.0212 0.427 -56.1064 -6.2844 146.2918 8 0.8587 -0.4117 -0.1036 1.284 -0.9756 0.9174 -0.0494 -0.0922 -0.2131 -0.0421 0.0961 -0.0511 0.2308 0.0685 -0 0.4842 0.0404 -0.0941 0.3424 0.0343 0.3213 -75.334 9.0392 235.8936 9 0.1399 0.1617 0.4275 0.1431 -0.5529 1.2188 0.0194 0.0515 -0.0179 0.1745 0.027 -0.1216 0.1773 0.0098 0 0.3892 0.0536 -0.0405 0.3091 0.0113 0.2632 -75.8167 21.1388 226.3123 10 0.2306 0.1003 0.4919 0.8972 0.2056 1.0311 -0.0915 0.1056 -0.3084 0.207 -0.1224 0.4125 0.4403 -0.326 -0.0001 0.4299 -0.0927 0.0886 0.3933 -0.0599 0.4517 -96.0507 12.334 210.6065 11 0.7004 0.1072 -0.1032 0.2306 -0.2307 0.9412 -0.0041 -0.0445 -0.2585 -0.0136 -0.0047 0.0289 0.1556 -0.1042 -0 0.3573 0.0087 -0.0125 0.3184 0.0418 0.3537 -87.0789 12.904 222.7187 12 1.0079 0.2416 0.2789 2.6046 0.3864 0.6838 0.0235 -0.0356 -0.0005 0.0599 0.0231 -0.2192 -0.0733 0.0256 0 0.2265 -0.0145 -0.0062 0.186 0.0081 0.3387 -51.0991 33.8513 273.1049 13 0.0239 0.1391 -0.345 0.728 0.127 0.1776 -0.0205 -0.0174 0.0239 0.0071 0.0147 -0.0353 -0.039 0.0407 0 0.2411 -0.0078 -0.0338 0.1771 0.0162 0.3215 -56.965 17.6867 273.847 14 0.9093 0.649 -0.1528 1.3492 -0.2223 1.1273 -0.0753 -0.2138 0.1456 0.3093 0.0359 0.1793 -0.0925 -0.1659 0 0.3112 0.0526 0.011 0.2766 -0.0359 0.3445 -74.0822 12.0161 287.8998 15 0.1497 -0.148 -0.2537 1.0746 -0.5652 0.1017 -0.0247 -0.045 0.0817 0.1463 0.0817 0.049 -0.0236 -0.0562 0 0.2914 0.0007 -0.0238 0.2291 -0.0031 0.3761 -64.1251 21.7815 278.6636 16 1.1744 -0.2784 -0.4678 0.8919 0.7232 1.8349 -0.0312 0.1272 0.0275 -0.0941 0.0187 -0.0081 -0.0173 0.0374 0 0.2223 -0.0069 -0.0082 0.2934 -0.04 0.2614 -22.6074 55.2784 237.8744 17 0.2271 -0.3099 0.105 0.9422 0.906 1.1391 0.0041 0.0986 -0.0185 -0.0372 0.0034 -0.0159 0.033 0.0409 -0 0.2476 -0.0201 -0.0002 0.28 -0.0232 0.2714 -25.6358 61.4647 250.5321 18 1.034 0.2041 -0.312 1.26 0.0436 1.1204 -0.1567 0.215 0.21 -0.2313 0.1588 0.2789 -0.1157 -0.2269 -0 0.315 -0.016 -0.0937 0.3075 0.0174 0.3059 -45.3954 77.993 248.7806 19 0.6151 -0.3678 0.0993 1.1788 1.4392 0.8919 0.0065 0.1583 0.0283 -0.1453 -0.1098 0.0876 -0.1471 -0.0734 0.0004 0.2701 0.001 -0.021 0.3271 -0.0144 0.2536 -35.8262 66.4967 244.1764 20 0.624 -0.5275 -0.156 0.649 0.082 0.7077 0.2752 0.4936 0.0661 -0.235 -0.1476 -0.209 0.1483 0.1612 0.0003 0.3511 0.0787 0.0372 0.4797 -0.0122 0.4925 -26.9864 3.6449 252.168 21 1.0547 0.2506 -0.7268 0.2993 -0.0658 0.5284 0.0559 0.0583 -0.0164 0.0288 0.0228 -0.1469 0.0052 0.0822 0 0.1807 0.0098 -0.0191 0.1898 0.0258 0.3544 -37.2913 4.623 263.6844 22 1.4239 -0.4661 0.3333 1.3903 -0.3739 0.6914 0.0063 0.0688 -0.0697 -0.0643 -0.0208 -0.0922 0.024 0.086 0 0.2473 0.0007 0.0193 0.2086 0.0142 0.2808 -44.6965 -20.5689 266.0978 23 0.9866 0.5044 -0.0273 0.5381 0.105 0.3625 0.1872 0.1097 -0.3114 0.0974 0.0032 -0.2534 0.0685 0.0991 0.0812 0.286 0.0891 -0.07 0.3107 -0.0319 0.5128 -26.1901 -6.8475 263.6217 24 0.8004 0.9806 0.4436 1.294 1.2423 1.4142 0.0328 0.1693 -0.1829 -0.0437 0.089 -0.1877 0.4607 -0.0336 0.0014 0.4382 0.0304 -0.0402 0.4615 -0.08 0.2737 -85.5091 13.3448 169.9142 25 0.434 0.0554 0.4513 0.7734 0.168 1.4648 -0.0084 0.1412 -0.0501 -0.152 0.0062 0.0026 0.0373 -0.0041 0 0.289 0.0186 0.001 0.4062 -0.0545 0.233 -81.373 23.4158 183.1469 26 0.5667 -0.0746 0.0222 0.6018 -0.0159 0.3486 -0.0682 0.1285 -0.3466 0.11 0.0134 -0.2723 0.2598 0.3145 -0.0003 0.4039 0.115 0.0113 0.5341 -0.0988 0.4804 -60.9746 12.6594 194.9477 27 0.8168 0.5115 -0.0832 0.3046 -0.0455 0.0548 -0.0771 0.1082 -0.3595 0.0305 0.057 -0.0456 0.2523 0.0514 -0 0.4418 0.0597 -0.0132 0.365 -0.0786 0.3767 -75.3629 9.3795 200.0612 28 0.5776 0.4772 0.0663 0.1925 0.0728 1.073 0.1144 0.273 -0.3116 -0.2789 0.0252 -0.2351 0.1264 0.3714 -0.0115 0.3902 0.1111 -0.0074 0.596 -0.1586 0.3941 -71.4656 18.4028 174.4802 29 1.1216 -0.2324 -0.5478 0.3933 -0.6113 1.8262 -0.1605 -0.2501 0.0011 0.1578 -0.0464 -0.0707 0.1801 0.099 -0.0129 0.4986 0.012 0.0702 0.429 0.0957 0.3092 -60.5102 59.1618 174.6303 30 0.1709 0.1685 -0.4883 0.4243 -0.3317 1.3755 -0.0945 -0.0715 -0.0365 -0.0169 -0.0088 0.0148 0.233 -0.0586 -0.0006 0.4601 0.0217 0.0797 0.3807 0.0956 0.3533 -60.0896 62.987 159.5772 31 0.9723 -0.1842 -0.2738 1.4924 0.1391 1.4656 -0.1432 -0.2809 0.1237 0.3142 0.1192 -0.2945 -0.0207 0.3047 0.0001 0.4029 0.0252 -0.0337 0.4154 0.0355 0.29 -41.3709 81.4429 159.732 32 0.6405 -0.083 -0.7015 0.8479 -0.1287 0.6078 -0.0679 -0.3614 -0.1001 -0.0019 -0.0301 -0.2016 0.3275 0.3865 -0.0275 0.3873 0.0782 0.0393 0.5969 0.1713 0.3342 -46.5202 60.5392 167.8343 33 0.5162 0.3699 -0.1651 0.9878 0.2864 1.6477 0.651 1.0789 0.563 -0.1481 -0.5286 0.158 -0.4105 -0.8565 0.1081 0.4205 0.3597 -0.0876 0.9498 0.0952 0.5523 -30.4538 47.811 185.5552 34 0.7252 -0.0174 -0.2834 0.5746 0.5049 1.1226 0.0652 0.1484 0.0882 -0.0605 -0.1053 0.121 -0.2055 -0.222 -0.0011 0.2569 0.0533 -0.0163 0.3612 0.0029 0.2496 -16.2256 44.5326 205.1612 35 1.1176 0.2586 -0.3813 0.5825 0.3868 0.4607 0.3304 0.3764 0.2848 -0.1084 -0.3761 0.4436 -0.1293 -0.3437 -0.013 0.3127 0.1038 0.031 0.5612 -0.0425 0.4811 -32.2183 44.7448 200.9911 36 1.5363 0.3638 -0.5117 0.6712 0.4277 0.9473 0.1888 -0.2698 0.333 0.1413 -0.1385 -0.1117 -0.0347 0.1832 -0 0.3046 -0.0364 -0.1004 0.4735 -0.074 0.534 -52.3714 44.9976 225.3878 37 1.224 0.3085 0.0239 0.9533 0.3324 0.3314 0.026 -0.0671 0.048 0.1987 0.0699 -0.2167 0.0506 0.0461 0.0169 0.1763 0.0127 -0.0418 0.3205 -0.0098 0.2695 -62.6114 38.1711 217.5628 38 0.7468 -0.4758 -0.2751 0.7336 -0.0492 1.1468 0.1903 0.1625 0.1873 -0.1428 -0.0909 -0.0634 -0.1857 0.0887 0 0.3156 -0.0199 0.052 0.3885 0.045 0.2652 -66.8845 48.5843 194.2738 39 1.2004 -0.2786 0.2143 0.6537 0.1596 0.4696 0.1008 0.0561 0.1726 -0.0863 0.0118 -0.2555 -0.0517 0.109 0 0.2557 -0.0241 0.032 0.3631 -0.0114 0.3272 -59.4155 46.2756 207.9448 40 0.3184 -0.0646 0.363 0.8229 0.0689 0.3782 0.1053 -0.1368 -0.3227 0.1751 -0.0856 -0.2427 0.306 0.2395 0 0.549 0.1204 0.0112 0.604 0.0016 0.5731 -76.2875 -24.7706 136.1993 41 0.7426 -0.4129 -0.1614 0.5213 -0.2234 0.4839 -0.0057 -0.0044 -0.0665 -0.0749 -0.0484 -0.1059 0.1816 0.1883 -0 0.3988 0.0417 0.0503 0.3833 -0.0731 0.3491 -86.5659 -15.064 129.8321 42 0.349 0.495 0.5243 1.1898 0.609 0.8368 0.0249 -0.1522 -0.0104 0.1572 0.0373 -0.0953 0.0972 0.1183 0 0.4253 0.0347 0.0099 0.373 -0.0681 0.2881 -93.9839 -0.7996 150.6943 43 0.5041 -0.0202 -0.4063 0.2597 -0.0367 0.6103 0.2372 -0.2065 -0.0128 -0.0693 -0.1426 -0.1014 0.0811 0.3024 -0 0.4194 -0.0346 -0.0124 0.5211 -0.058 0.4513 -75.4001 -9.5839 139.9981 44 0.446 0.1547 0.2995 1.4586 -0.4599 0.3992 -0.0909 0.1064 0.2013 -0.2243 0.0317 -0.0084 -0.2415 -0.0807 0 0.553 0.0579 0.0435 0.2997 -0.0066 0.4185 -36.2155 37.9124 132.0163 45 0.6272 -0.2543 0.2093 1.2348 0.0914 0.543 0.0153 0.0314 0.079 0.0086 -0.0247 0.0688 -0.2597 -0.1359 0 0.3761 0.0216 0.0323 0.2674 -0.0346 0.3379 -34.011 22.9167 136.0931 46 1.4043 -0.216 -0.0744 0.9849 0.0799 0.9569 -0.1237 0.2229 0.2027 -0.2558 0.1677 -0.2362 -0.2007 0.2496 0.0001 0.477 -0.0959 0.068 0.4001 -0.0059 0.4026 -13.5609 15.9149 119.0944 47 0.5485 -0.1564 -0.2227 1.2907 0.1233 0.0223 0.0059 0.1443 0.2914 -0.1808 0.0585 -0.1683 -0.2107 0.0346 0 0.5022 -0.0172 0.0482 0.3651 0.0106 0.4805 -23.216 25.5125 126.9942
Refinement TLS group Show large table (4 x 47) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid -6 through 71 ) 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 72 through 297 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 298 through 345 )4 X-RAY DIFFRACTION 4 chain 'B' and (resid -3 through 71 ) 5 X-RAY DIFFRACTION 5 chain 'B' and (resid 72 through 168 )6 X-RAY DIFFRACTION 6 chain 'B' and (resid 169 through 297 )7 X-RAY DIFFRACTION 7 chain 'B' and (resid 298 through 345 )8 X-RAY DIFFRACTION 8 chain 'C' and (resid -2 through 71 ) 9 X-RAY DIFFRACTION 9 chain 'C' and (resid 72 through 168 )10 X-RAY DIFFRACTION 10 chain 'C' and (resid 169 through 273 )11 X-RAY DIFFRACTION 11 chain 'C' and (resid 274 through 345 )12 X-RAY DIFFRACTION 12 chain 'D' and (resid -3 through 82 ) 13 X-RAY DIFFRACTION 13 chain 'D' and (resid 83 through 194 )14 X-RAY DIFFRACTION 14 chain 'D' and (resid 195 through 273 )15 X-RAY DIFFRACTION 15 chain 'D' and (resid 274 through 345 )16 X-RAY DIFFRACTION 16 chain 'E' and (resid -2 through 82 ) 17 X-RAY DIFFRACTION 17 chain 'E' and (resid 83 through 168 )18 X-RAY DIFFRACTION 18 chain 'E' and (resid 169 through 273 )19 X-RAY DIFFRACTION 19 chain 'E' and (resid 274 through 345 )20 X-RAY DIFFRACTION 20 chain 'F' and (resid -3 through 71 ) 21 X-RAY DIFFRACTION 21 chain 'F' and (resid 72 through 168 )22 X-RAY DIFFRACTION 22 chain 'F'