Software Name Version Classification HKL-2000data scaling PHENIX1.10.1_2155refinement PDB_EXTRACT3.2 data extraction
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 5XYUResolution : 2.508→32.984 Å / SU ML : 0.31 / Cross valid method : FREE R-VALUE / σ(F) : 1.36 / Phase error : 30.85 Rfactor Num. reflection % reflection Rfree 0.2512 1998 5.45 % Rwork 0.2105 - - obs 0.2128 36673 99.09 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 ÅDisplacement parameters Biso max : 224.9 Å2 / Biso mean : 78.872 Å2 / Biso min : 30.25 Å2 Refinement step Cycle : final / Resolution : 2.508→32.984 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6063 0 0 32 6095 Biso mean - - - 60.22 - Num. residues - - - - 793
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 6165 X-RAY DIFFRACTION f_angle_d0.926 8356 X-RAY DIFFRACTION f_chiral_restr0.051 982 X-RAY DIFFRACTION f_plane_restr0.005 1060 X-RAY DIFFRACTION f_dihedral_angle_d15.582 3696
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 (%)2.5084-2.5711 0.3085 128 0.2934 2233 2361 89 2.5711-2.6406 0.3586 144 0.2731 2484 2628 100 2.6406-2.7183 0.3224 143 0.2749 2472 2615 100 2.7183-2.806 0.3535 143 0.2743 2479 2622 100 2.806-2.9062 0.307 143 0.266 2493 2636 100 2.9062-3.0225 0.3287 142 0.2498 2480 2622 100 3.0225-3.1599 0.3116 144 0.2445 2507 2651 100 3.1599-3.3264 0.2603 144 0.2444 2492 2636 100 3.3264-3.5346 0.2999 143 0.2341 2481 2624 100 3.5346-3.8071 0.2432 143 0.2075 2496 2639 100 3.8071-4.1896 0.2201 145 0.1919 2498 2643 100 4.1896-4.7942 0.2091 145 0.1725 2515 2660 100 4.7942-6.0342 0.2212 144 0.1917 2501 2645 100 6.0342-32.9873 0.2138 147 0.1773 2544 2691 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 33) 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 2.8666 0.5768 0.8012 4.2302 -0.3349 5.7917 -0.0377 -0.003 0.3367 -0.9352 -0.3085 -0.0612 0.7526 -0.063 0.3862 0.577 -0.0366 0.0738 0.4631 0.0181 0.4678 -22.7175 6.9903 225.1096 2 3.6732 2.8197 -0.1488 4.3236 -0.2881 5.3722 0.0798 0.9523 -0.6169 -1.6044 0.2917 0.9827 2.7664 -0.0093 0.3541 1.7186 -0.1449 0.1334 0.6827 -0.0622 0.4577 -26.7018 -4.0639 217.8115 3 1.641 0.7023 -1.2445 1.5224 0.5965 2.3122 -0.1349 0.2903 -0.3738 -0.5733 -0.1322 0.2558 2.1328 -0.3306 0.3595 1.6451 -0.1918 0.0158 0.6794 -0.0449 0.7583 -26.1444 -12.45 230.7605 4 1.635 0.1853 -0.0665 1.867 0.4353 1.8599 -0.3475 -0.8407 -1.4007 0.1646 0.4667 0.6101 1.4381 -1.5653 -0.4044 1.0513 -0.2324 -0.3013 1.3679 -0.0121 1.3535 -44.2543 8.4791 225.144 5 2.3727 0.588 -1.7735 2.6909 1.6368 5.1762 -0.0235 -0.2603 -0.0317 -0.1005 -0.2624 0.2274 1.0174 -0.007 0.4172 0.4758 -0.1262 0.0645 0.4596 -0.0047 0.5189 -24.0927 1.7169 235.3116 6 1.6414 0.5662 -0.6906 2.3003 -0.6733 5.7134 0.2281 -0.7598 -1.2601 -1.3271 0.0531 0.8571 2.6049 -0.286 -0.2601 2.0466 -0.2945 -0.142 0.6198 -0.0943 0.8055 -28.5089 -13.8137 229.5066 7 2.1818 -1.0922 -0.3952 3.6253 1.1539 0.5356 0.1702 -0.7437 -0.6248 0.0258 0.3252 1.4292 1.6122 -1.5237 -0.2133 1.1101 -0.5276 0.0037 0.9955 -0.0576 0.7943 -35.2822 -1.6276 233.2277 8 1.873 0.5346 -1.2936 3.2818 -0.5727 4.4808 0.019 -0.3794 -0.3853 0.4036 0.0415 0.2891 -0.3963 -0.0635 0.0199 0.4479 -0.115 0.0359 0.5248 0.0429 0.4292 -25.8225 8.1083 252.1495 9 2.1061 0.0229 -0.3417 2.3211 -2.2129 3.0398 -0.0483 -0.1497 -0.0611 0.1687 -0.3969 -0.511 -0.2294 0.5998 0.3602 0.3751 -0.0594 -0.0619 0.5071 0.0446 0.4863 -19.394 13.7431 238.3269 10 3.5792 0.1648 -0.686 3.8813 -0.7444 5.7689 0.0543 -0.7801 -0.5528 1.3433 -0.9319 -0.8434 -1.2181 1.2046 0.3312 0.9904 -0.2963 -0.1664 0.7398 0.186 0.5946 -16.0753 14.612 257.148 11 3.4767 1.2166 -1.0133 3.5009 -0.6221 3.4363 0.0188 -0.6445 0.0222 0.7246 0.357 0.5895 -0.7608 -0.5716 0.0779 1.0728 0.0651 0.0881 0.589 -0.0402 0.5225 -29.267 18.2864 254.7368 12 0.2449 0.025 0.0938 4.4363 3.5871 2.957 0.728 0.7633 0.3332 1.9681 -1.3641 0.9019 -2.7408 0.2633 0.0709 2.067 -0.0536 0.0197 0.7471 -0.0376 1.0498 -35.5534 40.7546 250.0433 13 1.4769 -1.0018 -0.8446 6.4209 -2.9206 3.9622 -0.2151 -0.7476 -0.1633 1.4107 0.6812 0.6053 -0.9701 -1.0125 0.1687 0.7661 -0.0416 0.1204 0.7082 -0.1091 0.6135 -28.6624 11.0043 256.2978 14 3.2506 -0.3568 3.3527 5.2558 -1.485 7.6229 -0.0226 -0.7696 -0.485 -0.0295 0.1509 0.3352 0.8636 -0.764 -0.1332 0.5039 -0.0947 0.1887 0.5962 0.0608 0.6162 -24.5409 -2.598 251.8905 15 3.3407 1.003 -0.7029 5.9857 -2.1272 4.6826 0.5263 -0.714 0.724 0.5845 0.317 1.651 -1.9474 -1.3652 -0.4876 1.3113 0.415 0.1689 0.7753 0.0784 0.819 -33.0069 25.42 237.4211 16 2.8987 1.0451 -0.79 5.3697 -0.8319 5.9831 0.4094 0.1584 0.133 0.686 -0.3744 -0.6051 -0.9853 0.2717 -0.502 0.7853 -0.1375 -0.001 0.4775 -0.0447 0.5648 -22.0988 22.9083 239.9697 17 1.2306 0.9323 -1.6431 1.1455 -2.3194 6.1995 0.3857 -0.2481 0.1123 1.3418 -0.0599 0.2064 -1.7122 -0.4182 -0.1107 1.4654 -0.3249 0.1048 0.6988 -0.0879 0.4149 -25.7159 18.2264 257.4287 18 1.6469 0.1606 -1.9469 8.3793 -1.4349 2.6715 0.821 0.202 0.9735 -0.5605 0.0335 1.0577 -0.4853 0.7012 -1.0534 1.5567 0.065 0.0635 0.9203 0.1424 1.1967 -37.1569 5.5091 271.132 19 2.0037 1.2383 -4.2205 7.2789 3.3947 3.6716 -0.1867 0.6333 1.7987 -0.0084 -0.3823 1.3866 -3.2895 -3.459 1.2671 2.3285 0.3659 -0.5101 2.5184 -0.3837 1.2556 -49.6037 -7.0621 270.3741 20 2.9767 -0.7018 0.8689 2.7326 0.275 3.6017 -0.1477 -0.2982 -0.7811 0.1781 -0.04 0.3125 0.1392 -0.4041 0.0571 0.3011 0.0493 0.026 0.4943 0.0209 0.5372 -28.5289 45.7953 221.4646 21 4.2793 -0.3094 -1.0338 1.5329 -2.3879 4.4808 0.072 0.3284 0.1481 0.8587 -0.3862 -2.7213 -0.5962 1.0745 0.4499 0.5026 -0.0958 -0.1298 0.7746 0.1461 0.669 -8.7237 46.0654 216.2929 22 1.338 -1.1343 -1.3823 5.1998 0.1075 1.5713 -0.3546 -0.1102 -0.5783 1.6384 -0.1732 -0.7327 0.26 0.4151 0.4321 0.6283 -0.0423 -0.0318 0.5062 0.0724 0.5225 -18.1759 39.9157 222.1283 23 3.2321 -1.0869 -2.8628 3.6132 0.2143 5.0828 0.5216 -0.2038 0.5141 0.3741 -0.0781 0.1429 -1.2393 -0.1962 -0.3064 0.6754 0.0621 0.0115 0.5232 -0.0064 0.5294 -25.3612 60.0182 219.5227 24 0.0721 0.0904 0.1757 0.0613 0.0939 0.7397 -0.2228 -1.3809 0.0109 0.1017 0.135 0.5112 0.2214 -1.7639 0.3288 0.7317 -0.0258 -0.3126 1.1248 0 1.471 -39.7174 40.464 213.4402 25 1.1278 0.0657 -1.2957 2.316 -1.1942 2.5178 -0.0875 0.3098 0.0134 -0.0388 -0.0927 0.5046 0.1447 -0.1865 0.2388 0.232 0.036 -0.1622 0.4707 -0.0108 0.5386 -24.0218 43.8067 211.2992 26 1.4963 -2.1395 -1.8694 4.2433 0.0448 6.4391 0.6654 -0.261 1.333 0.6457 -0.2597 -0.1137 -1.5669 0.5026 -0.0309 0.8474 -0.1571 0.0954 0.48 -0.0515 0.7818 -14.852 62.4449 214.2544 27 4.3059 0.0763 0.8698 2.4406 0.3272 0.3187 0.7124 0.1085 1.1699 -0.9797 0.1318 2.3574 -0.6599 -1.2957 -0.3387 1.0441 0.2696 0.1479 0.6946 0.145 1.3642 -29.0997 67.6677 208.9803 28 2.0432 -0.4292 0.1718 2.7209 1.936 1.588 -0.303 1.1882 0.6726 -1.4782 0.3109 1.0489 0.1777 -0.8899 -0.1947 0.3909 0.2237 -0.1091 0.8207 0.1259 0.709 -30.7772 52.3354 208.5003 29 1.6274 0.1318 -1.3749 5.3254 -1.8603 3.9184 0.1308 0.1383 -0.0228 -0.6265 -0.2795 -0.0802 0.3234 0.3139 0.1161 0.3314 0.1075 -0.0053 0.4705 0.0803 0.4023 -14.2774 39.948 202.9386 30 1.803 0.2291 1.1345 4.3862 0.9503 0.7381 -0.1926 0.1449 -0.0044 -1.0832 -0.1827 -0.3827 0.4097 0.0948 0.4016 0.9935 0.0841 0.2737 0.6306 -0.002 0.5705 -11.4146 30.9623 192.4445 31 1.7334 0.644 -0.7247 6.0969 1.4671 4.5245 0.2409 0.4346 0.1488 -0.5958 -0.1524 -0.1455 -0.1508 -0.1073 -0.1098 0.6275 0.1441 -0.0667 0.5215 0.0802 0.4353 -14.4057 48.2228 193.3239 32 2.4836 -0.3959 -2.2157 4.0765 -1.2515 6.7596 -0.1702 0.3023 -0.2989 -0.7804 -0.1733 -0.0515 1.3992 -0.4278 0.3981 0.8949 0.0512 0.0554 0.4824 -0.0624 0.5957 -19.7959 28.3191 202.9545 33 0.2935 0.4296 0.3751 1.4659 1.2103 1.1517 -0.6879 -0.6434 0.3217 1.2406 0.4452 0.4737 1.3568 -0.9388 0.3499 1.3639 0.024 0.14 1.1694 0.1073 1.1933 -25.5567 52.2451 172.6019
Refinement TLS group Show large table (6 x 33) 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 6 through 58 )A6 - 58 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 59 through 78 )A59 - 78 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 79 through 103 )A79 - 103 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 104 through 114 )A104 - 114 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 115 through 147 )A115 - 147 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 148 through 168 )A148 - 168 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 169 through 190 )A169 - 190 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 1 through 31 )B1 - 31 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 32 through 69 )B32 - 69 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 70 through 90 )B70 - 90 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 91 through 106 )B91 - 106 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 107 through 114 )B107 - 114 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 115 through 133 )B