Software Name Version Classification PHENIX1.17.1_3660refinement DENZOdata reduction SCALEPACKdata scaling PDB_EXTRACT3.27 data extraction PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 2h5qResolution : 1.93→49.97 Å / SU ML : 0.18 / Cross valid method : THROUGHOUT / σ(F) : 1.34 / Phase error : 18.87 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.191 1975 2.96 % Rwork 0.1613 64684 - obs 0.1621 66659 98.42 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 330.85 Å2 / Biso mean : 47.3459 Å2 / Biso min : 20.76 Å2 Refinement step Cycle : final / Resolution : 1.93→49.97 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 5324 0 28 507 5859 Biso mean - - 266.14 47.3 - Num. residues - - - - 678
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 (%)1.93-1.98 0.2499 131 0.2592 4327 4458 93 1.98-2.03 0.2722 139 0.2275 4692 4831 100 2.03-2.09 0.2808 148 0.2176 4694 4842 100 2.09-2.16 0.2214 139 0.1979 4633 4772 100 2.16-2.24 0.2212 139 0.1875 4671 4810 100 2.24-2.33 0.2047 149 0.172 4689 4838 100 2.33-2.43 0.1822 141 0.1673 4630 4771 99 2.43-2.56 0.2224 144 0.1701 4608 4752 98 2.56-2.72 0.1882 143 0.1685 4655 4798 100 2.72-2.93 0.2093 140 0.1702 4675 4815 99 2.93-3.23 0.2048 143 0.1679 4664 4807 99 3.23-3.69 0.1799 132 0.149 4574 4706 97 3.69-4.65 0.156 142 0.1283 4618 4760 98 4.66-49.97 0.1754 145 0.1536 4554 4699 95
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 58) 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 8.9984 3.9966 -8.0017 5.3725 -3.609 7.1135 0.7458 1.2955 1.9539 -0.8239 0.2808 1.9902 -0.8016 -1.3705 -0.8679 0.5301 0.1303 0.0393 0.4891 0.2065 0.8237 -13.585 -4.995 -7.235 2 8.1009 -6.0358 4.0517 5.0798 -5.1636 7.3429 -0.213 -0.002 0.2568 0.718 -0.0649 0.4339 -0.5646 -0.1782 0.1409 0.241 -0.0363 0.0106 0.2457 -0.0669 0.2703 -4.485 -19.884 7.441 3 6.2825 -5.3892 5.3682 7.9829 -5.3954 7.868 -0.1131 -0.1599 0.4197 0.4566 0.0479 0.2464 -0.4439 -0.1135 0.018 0.2797 -0.0258 0.0486 0.2822 -0.0655 0.3766 -1.922 -17.282 7.8 4 2.9398 -2.6086 3.8514 7.4408 -6.2092 9.0892 -0.0298 0.092 0.5392 0.0299 -0.0647 -0.1436 -0.46 -0.1607 0.1159 0.234 0.0231 0.0513 0.2798 -0.0122 0.4403 -1.177 -13.013 2.143 5 4.1153 1.3253 3.4117 1.7157 1.8666 3.2663 -0.0658 -0.0349 0.2785 -0.1079 0.0657 -0.027 -0.4131 -0.148 -0.0269 0.3033 0.0039 0.0322 0.2641 0.0061 0.3016 4.193 -24.68 6.14 6 2.3254 1.4693 -1.6704 4.3408 -0.7812 7.3722 0.2044 0.7246 0.4273 -0.4866 -0.2182 0.3828 -0.2292 -0.396 -0.0226 0.4054 0.1361 -0.0897 0.4516 0.0296 0.48 -13.404 -15.761 -10.503 7 8.9725 -6.0039 -1.3337 4.7169 0.5619 1.499 0.1278 0.1922 -0.0449 -0.0943 -0.1216 0.3502 -0.0482 -0.1993 -0.0135 0.237 -0.0185 -0.017 0.2623 -0.0239 0.3101 -6.928 -28.049 0.272 8 8.6756 -6.9393 1.0334 7.5273 -1.1819 2.2702 -0.3493 -0.3754 0.3294 0.7484 0.2218 0.2241 -0.2116 -0.2494 0.0528 0.2178 0.0088 -0.0002 0.2709 -0.0827 0.2632 -9.032 -20.496 5.607 9 7.3375 -2.6309 1.6483 8.9643 -5.0838 3.4606 0.1537 0.0579 0.1022 -0.1458 -0.3188 -0.4415 0.2501 0.4771 0.18 0.2516 0.0048 0.0356 0.2125 -0.0599 0.2184 10.635 -31.478 1.896 10 4.7384 4.3415 1.6455 3.9163 1.5245 7.7359 0.0476 0.4606 -0.7657 -0.8074 -0.3393 0.1819 0.6927 -0.1505 0.2189 0.4331 0.0694 -0.0683 0.4198 -0.0329 0.474 -9.813 -29.152 -13.352 11 4.0167 -0.7427 4.8825 3.1452 0.0809 6.3825 0.3361 0.5077 -0.0184 -0.0652 -0.2006 -0.1246 0.2365 0.3874 -0.2234 0.3369 0.0327 0.0303 0.2472 -0.0076 0.2774 4.349 -29.977 -7.586 12 3.3089 -3.762 -1.3185 5.3726 0.8787 0.7545 0.0387 0.9166 -0.8748 -0.1817 -0.2499 0.4782 0.2082 -0.1521 0.2355 0.3121 0.0123 -0.0071 0.3726 -0.0293 0.2473 -1.982 -31.215 -6.546 13 4.8963 0.517 1.0041 2.7827 0.6396 3.8735 0.1645 0.5366 0.3309 -0.3365 -0.1659 0.1086 0.039 0.0846 0.0445 0.315 0.0583 0.0123 0.1311 0.0346 0.2931 -1.838 -19.587 -4.404 14 3.0272 1.9822 2.0515 3.6361 2.2253 2.2875 -0.2916 1.107 0.0632 -0.8202 0.2464 -0.1741 -1.1485 0.8705 -0.2042 0.4855 0.0854 0.0825 0.5423 0.0335 0.4698 -0.339 -17.278 -11.581 15 8.8355 1.0059 -0.9575 6.5118 3.0112 8.9665 -0.0046 -1.3303 -1.6641 1.1644 -0.5529 -0.1122 1.2322 0.0543 0.4613 0.8899 -0.0165 0.0921 0.6794 0.255 0.7467 -22.629 -24.501 32.718 16 6.6459 -2.5175 1.598 1.1333 -0.2835 6.8233 -0.0544 -0.5348 -0.7028 0.7434 0.2958 0.9334 0.1211 -0.4328 -0.4328 0.2296 -0.0369 0.0558 0.3298 0.0208 0.271 -33.203 -7.746 19.507 17 2.3285 -5.2432 4.5533 4.1084 -3.178 6.2597 0.1813 0.3009 -0.2796 0.0396 -0.3508 -0.1075 0.2285 -0.0658 -0.1103 0.2363 -0.0288 0.0184 0.4146 0.0457 0.5993 -33.132 -9.312 16.647 18 8.5657 -4.5429 6.4985 7.2414 -3.7647 6.0066 -0.0078 -0.4676 -1.3223 0.0919 0.3647 0.2762 0.3766 -0.2426 -0.4273 0.3152 0.0066 0.089 0.328 0.079 0.3336 -26.029 -14.239 18.415 19 7.1577 2.252 5.4484 5.1668 2.389 5.8721 0.0653 -0.0028 -0.1032 0.0665 -0.0231 0.1212 0.1308 0.0768 -0.0788 0.237 0.0178 0.0257 0.2891 0.0174 0.2868 -29.289 -2.37 11.819 20 6.5391 -2.4513 2.678 4.5044 0.4857 3.907 -0.1894 -0.5721 -0.1762 0.697 0.0422 -0.2426 0.5075 0.3119 0.2002 0.612 0.0637 -0.0323 0.5831 0.1687 0.3424 -19.066 -11.587 33.724 21 3.0957 2.3591 -3.3134 9.8871 -7.0633 9.0206 0.0883 -0.364 -0.1612 0.5747 0.0828 0.3813 -0.0764 0.0035 -0.1525 0.3043 0.0008 -0.0003 0.358 -0.0019 0.248 -27.563 0.658 24.37 22 3.8543 -0.6488 -0.2481 9.1189 -4.7213 5.7684 0.0199 -0.1344 -0.4693 0.0421 0.1982 0.9929 0.48 -0.4854 -0.295 0.3227 -0.0312 0.0596 0.4102 0.024 0.326 -32.914 -7.249 24.308 23 9.8837 -5.8067 -7.089 4.3489 6.1385 9.5692 0.1672 0.3956 0.6406 -0.1642 0.038 0.067 -0.5642 -0.1966 -0.1612 0.3691 0.0113 -0.0159 0.3043 0.0385 0.3384 -27.968 9.684 6.878 24 5.204 -6.4582 5.119 8.1027 -6.517 5.338 0.2704 0.5899 -0.0087 -0.4957 -0.3568 -0.3349 0.457 0.5552 0.2498 0.2847 0.0093 0.0459 0.35 0.0125 0.3012 -19.166 0.392 7.625 25 7.0431 -5.4437 -5.8421 6.6452 5.6441 5.3389 0.1434 -0.5227 0.4441 0.1499 0.0984 -0.3824 -0.2223 0.3442 -0.1843 0.3931 0.0052 -0.0718 0.6415 -0.0116 0.3933 -15.736 2.135 32.094 26 5.5565 1.1764 -4.4056 3.4416 -2.5162 4.1922 0.032 -0.2132 0.0636 0.1603 0.2006 -0.0738 -0.2984 0.6796 -0.2433 0.2192 0.0215 -0.0295 0.2426 -0.0067 0.3181 -16.169 3.184 16.233 27 7.3045 5.3673 -6.2539 6.0121 -5.222 5.3696 0.3111 -0.7339 0.1007 0.616 -0.3537 -0.0801 -0.9034 1.1006 -0.0028 0.2609 0.0138 -0.0116 0.4195 0.0006 0.2657 -19.555 4.197 21.947 28 4.9321 0.4951 1.4789 2.2433 1.2738 7.0578 -0.2459 0.0432 -0.2266 0.3168 0.0483 -0.0968 0.1463 0.8449 0.1661 0.3281 0.0605 -0.0244 0.1736 0.074 0.3123 -20.604 -7.375 20.674 29 2.9216 4.1734 2.1831 6.8817 4.449 3.2806 0.6225 -0.2726 -1.5163 0.5599 0.3845 -0.9784 0.5632 0.6924 -0.8573 0.3283 0.0647 -0.007 0.6382 -0.0055 0.4139 -13.786 -9.652 21.757 30 6.0011 -5.7643 6.0502 5.5514 -5.8161 6.0887 0.3144 1.2727 -0.0332 -0.2311 -0.2674 -0.1613 -0.4627 1.1659 0.0779 0.424 0.0648 0.0235 0.5955 0.0124 0.4213 -46.394 1.818 -11.984 31 6.043 6.0322 -5.5485 7.5973 -6.5715 8.4613 1.0424 0.2577 -1.7697 -1.1667 -0.9415 0.4516 1.9546 2.1744 0.0145 0.4464 0.1995 -0.0366 0.5099 -0.0269 0.7751 -38.972 -15.224 2.047 32 6.3151 -5.9077 6.4194 5.3973 -6.0322 6.4536 0.3657 -0.0033 -0.0756 -0.7484 -0.0438 -0.1485 0.9832 0.5113 -0.1804 0.3105 0.0223 -0.0057 0.3325 -0.0415 0.3695 -42.201 -5.64 1.447 33 6.6187 -6.7261 5.3454 6.9071 -5.3962 4.3669 0.9854 1.499 1.9031 -1.266 -1.3391 -1.7573 -0.6243 1.5171 0.5591 0.6176 -0.0459 0.2498 0.6388 0.0623 0.5723 -46.562 8.795 -12.965 34 5.0462 -5.1564 1.3062 7.6739 -1.2267 3.3385 0.3264 0.7549 0.0275 -0.8515 -0.3423 -0.2191 0.3194 0.077 0.0365 0.2706 -0.0089 -0.0125 0.4035 -0.0215 0.3732 -54.297 2.778 -5.98 35 5.7533 -2.6339 -0.4143 8.4529 5.4444 6.9763 -0.0644 0.8179 -1.8511 -0.9585 -0.3764 0.1573 -0.1361 -0.7855 0.5191 0.6702 -0.1323 -0.1346 0.7575 -0.1669 0.977 -57.444 -14.091 -6.679 36 2.1838 -1.5931 -2.492 3.9673 -0.6779 5.0845 -0.1185 1.2431 -1.1201 0.0498 1.1772 -0.1447 0.3148 -0.8307 -0.9744 0.2051 -0.0693 -0.0667 0.3899 -0.0027 0.4875 -56.217 -3.999 -0.316 37 8.8628 -8.5241 6.988 8.9505 -5.6748 7.2142 -0.1467 -0.2068 -0.2454 0.3722 0.1626 -0.0086 0.0321 -0.3501 -0.0594 0.2268 0.0164 0.0184 0.3584 0.0036 0.3832 -56.137 5.722 2.903 38 6.7086 3.9038 4.3887 4.6787 0.2115 5.1414 0.5377 -1.302 0.2848 0.2248 0.1989 1.7558 0.7275 -1.6562 -0.8225 0.3821 -0.085 0.0023 0.5256 0.1758 0.5655 -56.966 -7.233 7.336 39 8.5149 -6.8295 -4.8348 7.084 6.4704 8.8528 -0.0831 -0.3512 -0.2843 0.2154 -0.7037 0.4666 0.3192 -0.7143 0.7952 0.3183 -0.0281 -0.0773 0.4174 0.017 0.4303 -49.759 -5.344 7.516 40 9.3738 7.591 -7.4719 9.8495 -6.7212 8.9735 0.502 -0.1775 0.8988 0.0755 -0.3117 0.0032 -1.0311 0.6907 -0.2216 0.4323 -0.0641 0.0211 0.4222 -0.0061 0.5132 -44.961 8.113 -2.231 41 0.6981 -1.8431 1.4061 7.3382 -2.1009 7.9516 0.1865 -0.1533 -0.1396 -0.3212 -0.2189 -0.1315 -0.0232 0.4405 0.0861 0.2305 -0.0003 -0.0074 0.3386 -0.0247 0.416 -44.947 -1.925 2.165 42 7.5851 -1.7344 5.3842 0.4583 -1.3274 3.9135 0.5519 -0.0459 -0.9778 -0.2201 0.0627 0.011 1.2176 -0.2325 -0.5629 0.4633 -0.0712 -0.0371 0.2913 -0.0256 0.5466 -48.111 -12.689 3.006 43 8.7181 0.0125 1.8309 9.2352 5.7888 4.0111 0.3295 0.5168 -0.3351 0.0568 1.6315 -0.8126 0.8802 0.3532 -1.7919 0.573 -0.0126 -0.0619 0.4563 -0.0461 0.391 -51.153 -4.427 -8.858 44 9.673 -8.8487 -1.2294 8.796 1.368 0.2294 0.2882 0.6955 -0.2865 -0.5079 -0.1286 0.4871 -0.2401 -0.3366 -0.131 0.2759 0.0296 0.021 0.3313 0.0531 0.382 -60.51 6.681 -5.56 45 9.4425 -6.0236 -7.3966 7.4437 7.5717 8.0925 0.1676 0.5017 -1.03 0.0922 -0.0322 -0.1029 -0.132 0.5146 -0.1342 0.3189 -0.0165 -0.043 0.3625 -0.0133 0.4153 -62.529 2.26 -8.501 46 5.9423 -5.965 3.2597 6.0644 -3.9084 9.3717 0.0751 1.0144 0.5603 -0.6499 0.215 -1.1845 0.3925 -0.2677 -0.2887 0.3876 0.0094 0.0273 0.5591 -0.0916 0.4573 -51.781 -1.194 -12.942 47 8.3218 -1.0224 1.7165 8.4303 -1.4409 1.95 0.1954 0.0588 -0.8955 -0.2975 -0.2102 -0.6834 1.8373 1.3096 -0.0653 0.585 0.142 -0.0332 0.4352 -0.1226 0.6394 -43.999 -14.469 -2.954 48 8.0942 -0.1171 1.4876 4.76 -4.5778 4.7919 0.5515 -0.212 -0.1418 0.1035 -1.0068 -0.6467 0.2098 2.6834 0.5655 0.4015 0.0024 0.0427 0.8973 0.0132 0.4039 -52.368 -30.269 31.515 49 9.7562 -5.3352 2.8268 8.997 -0.9717 4.917 0.1454 0.8431 1.4613 -0.3708 -0.627 -0.4324 -0.9532 0.4909 0.4968 0.62 -0.0679 -0.0052 0.3887 0.0325 0.4098 -65.056 -14.451 19.54 50 8.5157 -6.1095 6.1533 4.7748 -4.899 5.0609 -0.1353 -0.0246 0.2406 -0.096 -0.256 -0.7338 -0.1687 0.8381 0.5703 0.3572 -0.0138 0.0255 0.4965 0.0325 0.3826 -58.712 -28.638 25.441 51 1.3155 0.5001 -0.98 9.0686 -6.1659 5.6735 -0.0574 -0.2646 -0.0288 0.1163 -0.295 -0.6387 -0.0899 0.6408 0.2906 0.3968 -0.0502 0.0125 0.5619 -0.0275 0.3061 -61.151 -31.077 35.73 52 1.7775 -1.6161 -0.3772 5.3591 -4.4729 6.1142 0.1103 -0.3226 0.2983 0.9921 -0.2125 -0.8371 -1.0489 0.1747 0.1186 0.5192 -0.0543 0.0048 0.615 -0.0442 0.2807 -65.754 -23.803 36.858 53 5.6424 -3.2841 4.5358 2.0259 -3.01 7.6813 0.1321 -1.0907 -0.1314 1.0866 0.3648 0.8331 -0.6218 -1.3065 -0.4662 0.4872 0.0275 0.1215 0.5686 -0.0317 0.4035 -74.352 -23.161 32.745 54 7.0131 -4.9675 -4.2801 4.4238 4.0962 3.9822 0.1894 0.411 -0.274 -0.6322 -0.3712 -0.6393 0.7854 0.1732 0.0205 0.5044 0.0417 0.0632 0.4214 -0.0301 0.3793 -65.089 -33.112 25.665 55 8.9768 -2.9375 1.9439 3.732 -4.5058 5.8449 0.0169 -0.043 0.3292 0.2531 -0.1033 0.256 -0.4231 -0.1291 0.0046 0.364 -0.0455 0.0387 0.3087 -0.0512 0.2362 -67.372 -20.94 25.41 56 2.8591 -0.9633 1.9521 0.5332 -1.639 5.3461 -0.2333 -0.1609 0.1373 0.3563 -0.2226 -0.4143 -0.6983 0.7734 0.4024 0.4275 -0.0901 -0.0291 0.4783 -0.0162 0.2958 -61.38 -28.306 37.507 57 3.2829 3.2722 -2.9933 6.1368 -4.2934 7.5124 0.0746 -0.1519 0.0275 0.1507 -0.196 -0.2432 -0.4711 0.8502 0.1262 0.3802 -0.0754 0.0003 0.4941 -0.0009 0.2583 -59.711 -28.249 39.339 58 2.9551 -3.1138 -0.0121 4.796 3.6082 8.5314 -0.1565 0.626 0.8417 0.2219 -0.8636 0.4333 -1.6649 0.6881 1.1403 0.6987 -0.2203 -0.1091 0.4818 0.0664 0.5889 -61.994 -11.739 24.741
Refinement TLS group Show large table (6 x 58) 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 4:11 )A4 - 11 2 X-RAY DIFFRACTION 2 ( CHAIN A AND RESID 12:24 )A12 - 24 3 X-RAY DIFFRACTION 3 ( CHAIN A AND RESID 25:36 )A25 - 36 4 X-RAY DIFFRACTION 4 ( CHAIN A AND RESID 37:50 )A37 - 50 5 X-RAY DIFFRACTION 5 ( CHAIN A AND RESID 51:65 )A51 - 65 6 X-RAY DIFFRACTION 6 ( CHAIN A AND RESID 69:90 )A69 - 90 7 X-RAY DIFFRACTION 7 ( CHAIN A AND RESID 91:114 )A91 - 114 8 X-RAY DIFFRACTION 8 ( CHAIN A AND RESID 115:127 )A115 - 127 9 X-RAY DIFFRACTION 9 ( CHAIN A AND RESID 128:145 )A128 - 145 10 X-RAY DIFFRACTION 10 ( CHAIN A AND RESID 146:155 )A146 - 155 11 X-RAY DIFFRACTION 11 ( CHAIN A AND RESID 156:171 )A156 - 171 12 X-RAY DIFFRACTION 12 ( CHAIN A AND RESID 172:183 )A172 - 183 13 X-RAY DIFFRACTION 13 ( CHAIN A AND RESID 184:210 )A184 - 210 14 X-RAY DIFFRACTION 14 ( CHAIN A AND RESID 211:223 )A211 - 223 15 X-RAY DIFFRACTION 15 ( CHAIN B AND