Software Name Version Classification PHENIX(1.20.1_4487: ???)refinement HKL-2000data reduction HKL-2000data scaling PHENIXphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.58→30.57 Å / SU ML : 0.38 / Cross valid method : FREE R-VALUE / σ(F) : 1.36 / Phase error : 28.36 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2573 2017 2.84 % Rwork 0.2026 - - obs 0.2042 71007 97.55 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 2.58→30.57 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 16955 0 8 137 17100
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_dihedral_angle_d7.259 2298 X-RAY DIFFRACTION f_chiral_restr0.102 2571 X-RAY DIFFRACTION f_plane_restr0.018 3101
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.58-2.65 0.3836 92 0.3077 3831 X-RAY DIFFRACTION 76 2.65-2.72 0.358 159 0.2898 4950 X-RAY DIFFRACTION 99 2.72-2.8 0.324 145 0.2795 4993 X-RAY DIFFRACTION 99 2.8-2.89 0.3152 137 0.2644 4975 X-RAY DIFFRACTION 99 2.89-2.99 0.3097 158 0.2616 4972 X-RAY DIFFRACTION 99 2.99-3.11 0.3479 147 0.2422 4969 X-RAY DIFFRACTION 99 3.11-3.25 0.2601 143 0.2345 5017 X-RAY DIFFRACTION 99 3.25-3.43 0.2907 150 0.2239 5021 X-RAY DIFFRACTION 99 3.43-3.64 0.2696 164 0.2064 4983 X-RAY DIFFRACTION 100 3.64-3.92 0.2574 136 0.1905 5078 X-RAY DIFFRACTION 100 3.92-4.31 0.2208 146 0.1765 5021 X-RAY DIFFRACTION 99 4.32-4.94 0.2233 146 0.1553 5010 X-RAY DIFFRACTION 99 4.94-6.21 0.2338 145 0.1837 5054 X-RAY DIFFRACTION 99
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 7.7201 -0.0066 -0.308 1.6779 -0.3713 5.3407 -0.1884 -0.6496 1.1414 0.1769 -0.0768 1.1128 -0.4752 -0.2647 0.2983 0.4423 0.0201 0.0024 0.3549 -0.0633 0.5766 5.9919 2.4918 13.2232 2 4.1952 0.7718 1.6319 3.9633 -1.062 3.7672 -0.0038 0.1421 0.4138 -0.0646 -0.2051 -0.5219 -0.3315 0.6985 0.2469 0.4525 -0.1001 -0.0533 0.415 0.1662 0.5624 32.2957 1.8084 10.4486 3 9.8893 -1.4072 1.5095 3.6168 0.9814 3.5141 -0.043 -0.8187 -1.349 1.2928 -0.3053 0.6446 0.2121 0.0843 0.3461 0.4115 0.0896 0.0732 0.5022 -0.0202 0.4787 12.094 -9.8848 19.6472 4 1.5008 -0.9871 1.4407 1.3385 -0.0077 2.7203 0.0273 0.1657 0.077 -0.1619 -0.0978 -0.0665 -0.0421 0.0715 0.1046 0.2368 -0.0211 0.0559 0.2892 0.0673 0.2633 17.6036 -8.7326 4.413 5 5.3604 1.6458 2.0632 5.819 1.7812 2.8478 -0.4738 0.591 0.7079 -0.706 0.1973 0.3164 -0.5128 0.1629 0.2259 0.3047 0.0069 0.0032 0.3568 0.0973 0.347 11.1841 -0.34 1.2489 6 2.8295 1.3077 0.6135 3.1428 -0.5142 2.3638 0.0902 -0.077 0.0939 0.0988 -0.3149 -0.6106 -0.0765 0.0685 0.2729 0.2632 0.0007 0.0428 0.323 0.0429 0.3199 26.5304 -7.1603 12.6209 7 1.806 -1.9127 1.2878 3.9941 0.0686 3.8413 0.6076 -0.8264 -0.9203 0.8741 -0.3288 0.0027 0.4325 -0.6313 -0.3014 0.5134 -0.1391 -0.0163 0.4297 0.1449 0.3928 25.4747 -22.856 24.9872 8 1.985 -2.253 3.3191 5.8961 -1.1259 8.565 0.5926 1.1274 -0.7215 -1.4085 -0.6027 0.6556 1.0308 -0.2447 0.0518 0.8122 -0.0005 -0.0298 0.5601 -0.0685 0.618 19.8737 -48.6124 1.1889 9 0.5754 -0.5269 0.0468 1.8014 2.1258 3.5566 -0.0946 -0.0375 -0.417 0.7328 -0.3816 -0.2542 0.6219 0.0639 0.3434 0.7113 0.028 -0.0641 0.4575 0.1465 0.6766 32.3503 -45.11 24.3969 10 4.6801 0.1965 1.804 5.4117 -0.0654 3.4563 0.1931 0.251 -0.4437 -0.1064 -0.2498 -0.307 0.1987 0.484 0.0682 0.4257 0.0663 0.0926 0.3085 0.071 0.4245 29.5119 -36.6978 9.089 11 3.1949 -1.0982 -0.0453 4.59 -0.6113 2.2884 -0.0708 -0.4513 -0.5894 0.3922 0.0896 0.3534 0.7138 -0.1634 -0.0737 0.581 -0.0736 0.0025 0.3519 0.0426 0.4492 15.0608 -43.5272 14.7059 12 6.2806 -2.5376 3.4517 3.4156 -0.893 4.6228 -0.4797 -0.3899 1.2185 0.4598 -0.2843 -0.6262 0.029 0.0349 0.6651 0.3992 -0.01 -0.0342 0.3117 0.1243 0.4173 28.504 -25.9497 15.1223 13 2.9036 -0.4275 -0.8556 4.7338 2.5794 3.0324 -0.1234 0.3412 0.4296 -0.3916 -0.1115 -1.3309 0.0194 0.4157 0.2147 0.3038 0.0246 0.1376 0.4859 0.1576 0.5616 36.0241 -22.5927 6.5158 14 7.3334 1.653 1.1144 3.7504 0.8657 5.0942 -0.0413 -0.8705 0.3092 0.4965 0.1215 0.095 0.0675 0.065 -0.1159 0.517 0.0632 -0.0751 0.4383 0.124 0.4828 52.2866 15.4491 27.182 15 3.7451 -0.5193 -0.8135 5.7782 -1.9302 5.274 -0.0861 -0.8235 0.2849 0.4644 0.2818 -0.1534 -0.1398 0.1459 -0.1748 0.3403 0.0136 0.0028 0.2982 0.0185 0.4045 56.6082 21.2157 19.452 16 3.6831 0.4562 -0.6195 2.109 0.1474 2.4499 -0.0012 -1.0994 -0.6179 0.5991 -0.0193 -0.2383 0.2801 0.4016 0.0126 0.4754 0.0119 -0.0959 0.5642 0.1526 0.5155 62.162 9.6554 26.2425 17 1.5543 -1.9038 -1.36 3.226 -0.0305 5.5391 -0.1347 0.6485 1.2313 -0.1424 0.2499 0.1968 -0.5475 0.0493 -0.2267 0.4015 -0.076 -0.0492 0.4829 0.257 0.6548 57.3734 26.7178 4.499 18 6.6317 -3.9067 4.2427 5.9309 -3.5425 6.5104 -0.5036 -1.1663 0.7902 1.2884 0.0206 -0.113 -1.5338 0.1637 0.2005 0.6627 -0.089 0.0573 0.7067 -0.2314 0.9007 74.8674 -10.2464 -5.3719 19 5.1129 0.4186 1.5381 3.7888 -2.274 2.7699 -0.0355 -0.6081 -0.0976 -0.7009 0.4702 0.8992 0.7413 -0.6209 -0.286 0.6107 -0.1829 0.0036 0.7833 0.155 0.6084 56.3081 -29.8897 -11.9769 20 7.0727 2.3978 2.0108 5.3509 0.9654 5.9899 -0.2113 -0.4596 0.829 -0.2198 0.3347 0.1262 -0.539 -0.2754 0.0157 0.3511 0.016 -0.0529 0.504 0.0044 0.6154 64.1634 -16.3219 -19.2536 21 3.3165 -0.35 0.056 3.5261 -0.177 4.9382 0.2692 -0.4902 -0.0246 0.2519 -0.0394 -0.0704 0.5037 -0.0709 -0.1929 0.3301 -0.0478 -0.0639 0.4198 0.0638 0.4333 75.8901 -25.6309 -9.6077 22 2.2564 -0.8146 0.801 2.0019 -0.6105 2.3347 0.1284 -0.7963 -0.0039 -0.0193 0.2174 0.46 0.8864 -0.3237 -0.2669 0.5056 -0.1035 -0.0219 0.5702 0.2097 0.6448 65.1895 -26.0069 -17.6938 23 2.499 -1.052 -1.1205 2.5069 0.2345 2.782 0.1981 0.5152 1.364 -0.5687 -0.3778 -0.146 -0.813 -0.1461 0.0675 0.5468 0.0044 0.023 0.5696 0.252 0.8088 62.821 -12.2129 -34.4707 24 6.4608 2.1782 0.1125 5.1346 0.4577 2.5487 0.0533 -0.7596 1.1073 0.4807 -0.5067 0.3263 -1.3441 0.3814 0.4596 1.218 -0.184 -0.1284 0.5946 0.1049 0.6423 28.4822 -34.1104 -25.2756 25 2.0558 0.5011 -2.7577 0.1942 -0.7406 4.1064 0.4319 0.996 0.0063 -0.2117 0.0345 0.1607 -0.7069 0.9082 -0.2234 1.2704 -0.2095 0.2 1.1568 0.3192 1.0578 47.4394 -42.2276 -38.2943 26 1.686 -0.158 0.0676 3.7511 -1.7093 2.3208 -0.1848 -0.0696 0.4435 0.2158 -0.2601 0.0763 -0.9881 0.4312 0.2982 0.8036 -0.1585 -0.1069 0.4654 0.1221 0.5386 31.2665 -45.5741 -23.1515 27 0.9432 0.3839 -0.5329 2.3919 -0.759 2.0329 -0.1705 0.4876 0.7125 -0.2712 0.0992 0.2713 -0.8468 0.2114 0.0866 0.955 -0.1028 -0.1374 0.5419 0.1882 0.6343 27.2375 -39.3172 -38.4631 28 4.1829 0.5036 0.8006 1.2488 0.0286 0.1662 -0.0055 0.0451 0.4444 -0.213 -0.3068 -0.2725 -0.5487 0.6284 0.2313 0.6372 -0.0861 0.0325 0.6379 0.1686 0.3242 35.1968 -56.4087 -26.9539 29 1.3715 0.2403 1.4938 3.1628 0.8726 1.7819 0.1804 -0.2102 -0.1817 0.9372 -0.2617 -0.3046 -0.3682 0.3664 0.0964 0.6947 -0.1702 -0.0838 0.5257 0.1677 0.3812 32.8647 -59.46 -16.0132 30 5.8171 -0.7994 1.9493 5.2476 -1.5087 5.7085 0.7717 1.4226 -1.3332 -0.9332 -0.3256 0.0652 1.6074 1.0205 -0.2354 0.8894 0.1186 -0.0253 0.6663 -0.1512 0.66 26.1754 -8.3281 -35.3515 31 3.1277 0.9094 -2.1915 1.2343 -0.3454 4.4407 0.0074 -0.8049 -0.9716 0.1561 0.2355 -0.085 1.2662 -0.2462 -0.3402 0.7395 -0.0125 0.0408 0.7409 0.1693 0.5816 27.8406 -5.1433 -7.3711 32 6.5562 -0.334 -0.6823 6.0912 0.8401 3.1371 0.0652 0.5154 -0.393 -0.7302 -0.5677 -0.4233 0.5548 0.9418 0.4482 0.4518 0.0742 0.0802 0.5508 0.0356 0.3769 33.7653 1.4133 -34.2255 33 4.5297 -0.3863 0.0399 4.7375 0.3408 2.1528 0.2437 -0.3192 -0.3541 -0.0997 -0.3255 0.4387 0.3095 -0.1806 0.0122 0.3803 -0.0407 -0.0299 0.3292 0.0115 0.2965 19.9605 4.8255 -28.7024 34 5.7146 -3.5175 2.2904 6.1034 -1.6963 5.3078 0.374 -0.865 -0.8579 0.4267 0.1494 1.0014 0.6995 -0.9256 -0.4155 0.6653 -0.1721 -0.1493 0.5295 -0.0332 0.7162 10.6068 -2.487 -30.5289 35 3.8836 -0.2844 -0.0333 2.7861 0.239 3.8973 0.1443 0.1296 -0.9746 -0.3179 -0.2833 0.481 1.0193 -0.2426 0.2346 0.6058 -0.0221 -0.0248 0.3536 -0.0711 0.5211 19.8547 -5.8074 -27.866 36 8.1551 -0.0956 -1.2138 4.2921 0.9325 0.4662 0.0332 -0.1944 -0.2752 -0.0426 -0.2071 -0.8073 0.2609 0.8824 0.2735 0.523 -0.0531 -0.0028 0.7668 0.2263 0.416 38.665 9.1019 -28.5031 37 7.1238 2.1265 -0.4872 5.6066 3.1248 3.155 -0.4677 1.6088 0.4637 -0.91 -0.0268 -0.496 -0.7846 1.1655 0.7199 0.6084 -0.1457 0.0701 0.8088 0.2061 0.509 41.344 17.8018 -35.3717 38 4.8817 0.5084 0.4226 3.1556 -0.2808 6.4021 0.3063 1.8893 -0.5169 -0.8176 0.2105 -0.5405 0.7415 0.9415 -0.4593 0.6273 -0.0079 0.0319 1.1998 -0.1779 0.6559 83.1585 14.4291 -13.4683 39 0.1118 0.1954 -0.2985 5.3519 -3.5366 2.5941 0.3804 -0.2942 0.2061 0.2371 0.0594 0.0104 -0.1754 -0.7022 -0.0626 0.7457 -0.1261 -0.0271 1.3308 0.2304 1.1723 69.4554 35.4557 -13.8842 40 5.8501 0.6361 -0.1496 5.1428 -0.0697 3.7379 -0.0548 1.019 -0.7817 -0.8054 0.2688 -0.2584 0.7565 0.5465 -0.3453 0.4655 0.0428 0.0224 0.901 -0.2201 0.5854 73.2674 10.4944 -8.0728 41 2.8085 -0.2224 0.4577 2.5694 -0.0843 3.1106 -0.3119 1.2463 0.6006 -0.5176 0.3056 -0.4462 -0.4013 0.6629 0.0494 0.4406 -0.1304 0.011 0.8776 0.067 0.5971 79.6535 21.8136 -3.9708 42 2.1524 1.9891 -1.8842 5.4354 0.4255 9.1513 0.2119 0.2503 -1.5013 -0.0652 -0.0423 -0.7639 1.501 0.7762 -0.4057 0.5288 0.0083 -0.1434 0.6072 -0.0477 0.7762 60.1122 5.8271 3.5601 43 5.0787 -0.4443 1.7239 1.9768 -2.1051 4.7221 0.4816 1.1531 -0.2202 -1.3442 -0.2724 -0.386 1.628 1.0344 -0.0392 1.2424 0.2029 0.2504 1.2847 0.017 0.7423 72.8416 -27.1959 25.8072 44 0.7113 -0.7179 0.2781 3.467 1.6364 1.3986 -0.2931 1.6923 2.271 -1.8078 -1.2035 0.0184 -0.6066 0.3877 1.0822 1.278 -0.0498 -0.1572 1.2334 0.7798 1.6289 59.8708 -5.1817 23.063 45 2.5341 0.3164 -0.9478 2.4859 0.6215 4.6604 0.057 0.9174 0.2123 -0.8031 -0.0521 -0.6497 0.0733 1.5732 0.0389 0.7528 0.0957 0.1688 1.245 0.2428 0.7202 73.9151 -19.8364 33.9327 46 3.1415 1.0768 -1.0623 4.0947 -0.7591 6.1139 0.3514 1.3489 0.2323 -0.7995 -0.3171 0.4308 0.4829 -0.3742 0.0298 0.5732 0.1342 -0.0456 0.6238 0.074 0.5447 58.6331 -24.7884 36.8873 47 6.5767 2.582 -2.7901 5.5576 0.9213 6.9405 -0.0419 -0.0901 -1.2066 0.0265 0.1727 -0.1717 1.7503 -0.002 0.0267 0.7156 -0.0598 -0.047 0.4398 0.103 0.5941 54.5304 -32.9856 48.0956
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 'E' and (resid 1 through 35 )2 X-RAY DIFFRACTION 2 chain 'E' and (resid 36 through 88 )3 X-RAY DIFFRACTION 3 chain 'E' and (resid 89 through 103 )4 X-RAY DIFFRACTION 4 chain 'E' and (resid 104 through 152 )5 X-RAY DIFFRACTION 5 chain 'E' and (resid 153 through 203 )6 X-RAY DIFFRACTION 6 chain 'E' and (resid 204 through 252 )7 X-RAY DIFFRACTION 7 chain 'E' and (resid 253 through 282 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 3 through 35 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 36 through 73 )10 X-RAY DIFFRACTION 10 chain 'A' and (resid 74 through 116 )11 X-RAY DIFFRACTION 11 chain 'A' and (resid 117 through 224 )12 X-RAY DIFFRACTION 12 chain 'A' and (resid 225 through 237 )13 X-RAY DIFFRACTION 13 chain 'A' and (resid 238 through 282 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 3 through 78 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 79 through 116 )16 X-RAY DIFFRACTION 16 chain 'B'