Software Name Version Classification NB DENZOdata reductionShow SCALEPACKdata scalingShow REFMACrefmac_5.5.0054refinementShow PDB_EXTRACT3.004 data extractionShow SBC-Collectdata collection HKL-3000data reduction HKL-3000data scaling SHELXphasing MLPHAREphasing DMphasing ARP/wARPmodel building Cootmodel building
Refinement Resolution : 2→33.17 Å / Cor.coef. Fo :Fc : 0.963 / Cor.coef. Fo :Fc free : 0.948 / WRfactor Rfree : 0.244 / WRfactor Rwork : 0.192 / SU B : 7.896 / SU ML : 0.098 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.141 / ESU R Free : 0.134 / Stereochemistry target values : MAXIMUM LIKELIHOODDetails : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLYRfactor Num. reflection % reflection Selection details Rfree 0.217 1311 5.1 % RANDOM Rwork 0.182 - - - obs 0.184 25753 99.56 % -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.4 Å / Solvent model : MASKDisplacement parameters Biso mean : 15.043 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.1 Å2 -0.05 Å2 0 Å2 2- - -0.1 Å2 0 Å2 3- - - 0.15 Å2
Refinement step Cycle : LAST / Resolution : 2→33.17 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 2122 0 5 89 2216
Refine LS restraints Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.011 0.022 2181 X-RAY DIFFRACTION r_angle_refined_deg1.151 1.985 2943 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.341 5 272 X-RAY DIFFRACTION r_dihedral_angle_2_deg35.833 26.222 90 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.675 15 401 X-RAY DIFFRACTION r_dihedral_angle_4_deg5.954 15 2 X-RAY DIFFRACTION r_chiral_restr0.083 0.2 344 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.021 1583 X-RAY DIFFRACTION r_mcbond_it0.471 1.5 1372 X-RAY DIFFRACTION r_mcangle_it0.864 2 2206 X-RAY DIFFRACTION r_scbond_it1.457 3 809 X-RAY DIFFRACTION r_scangle_it2.281 4.5 737
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 20
Show large table (7 x 20) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.4-2.462 0.322 177 0.264 3514 3700 99.757 2.462-2.53 0.375 177 0.265 3439 3630 99.614 2.53-2.603 0.32 172 0.256 3354 3537 99.689 2.603-2.682 0.341 176 0.265 3237 3426 99.621 2.682-2.77 0.311 156 0.262 3149 3321 99.518 2.77-2.867 0.313 187 0.253 3030 3231 99.567 2.867-2.975 0.329 145 0.25 2939 3105 99.324 2.975-3.096 0.348 159 0.257 2841 3016 99.469 3.096-3.233 0.319 148 0.235 2697 2869 99.163 3.233-3.39 0.268 129 0.207 2615 2773 98.954 3.39-3.572 0.211 137 0.185 2443 2631 98.062 3.572-3.788 0.25 126 0.183 2307 2496 97.476 3.788-4.048 0.216 112 0.154 2181 2362 97.079 4.048-4.369 0.189 108 0.148 2018 2187 97.211 4.369-4.782 0.215 109 0.142 1876 2042 97.209 4.782-5.34 0.184 85 0.164 1742 1877 97.336 5.34-6.154 0.239 95 0.186 1493 1637 97.007 6.154-7.507 0.233 83 0.194 1277 1415 96.113 7.507-10.49 0.166 46 0.156 1039 1129 96.103 10.49-48.337 0.216 33 0.22 589 695 89.496
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 38) 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 14.6001 10.3781 -0.5002 21.9335 4.0835 17.5715 0.1744 -0.2938 0.1725 0.1169 -0.1347 -1.3008 -0.8542 1.3128 -0.0397 0.2348 -0.0223 0.0263 0.2365 0.0404 0.2207 5.2345 24.9102 57.8079 2 8.5059 8.8538 10.0781 9.1991 13.3159 22.6979 -0.0699 -0.2366 0.5126 -0.0397 -0.6348 0.5675 0.3032 -1.3628 0.7048 0.3095 0.07 -0.0484 0.2836 -0.06 0.3291 -7.3747 19.7489 49.1679 3 9.2245 6.7804 -0.5017 15.4329 5.7879 5.3613 -0.0196 0.3653 -0.0441 -0.8617 -0.2159 0.1323 -0.5648 -0.5542 0.2355 0.2962 0.0926 -0.0408 0.213 0.0267 0.1033 -10.26 27.9402 48.7022 4 14.2763 11.3597 2.1409 25.831 17.3193 14.7562 -0.0591 0.4999 0.7442 -0.0842 -0.3472 -0.1469 -0.4666 0.6428 0.4063 0.3139 -0.0245 -0.0084 0.3216 0.1509 0.3142 -1.6923 33.2403 52.7533 5 13.1935 -7.364 4.2273 34.1883 -5.4626 -4.6748 -0.5066 -0.301 1.3466 0.2646 0.3569 -0.4657 -0.1426 0.1109 0.1497 0.5394 -0.101 0.0707 0.5035 -0.0128 0.504 7.4792 31.8382 54.4302 6 10.0406 11.1999 2.9662 21.9365 2.5069 5.888 -0.1165 0.2876 -0.0371 -0.5683 0.2386 0.1541 0.4057 0.0673 -0.1221 0.2325 0.045 0.0279 0.1591 0.0421 0.1192 -1.8251 15.7227 50.1019 7 17.7415 10.3308 -7.1245 18.5114 -5.5068 1.2693 -0.0355 0.443 0.1848 0.3411 0.1343 -0.2892 -0.0885 0.0217 -0.0989 0.3341 -0.0442 0.0119 0.2708 0.0268 0.2666 -12.3888 0.8343 48.3685 8 6.362 7.5134 3.8907 6.4076 -2.4856 19.982 -0.5322 0.4769 0.6343 -0.576 0.684 0.9864 -0.7583 -1.0507 -0.1517 0.5198 -0.0231 -0.1199 0.5436 0.1356 0.319 -19.9339 -3.456 40.0005 9 3.8227 3.5396 -2.5301 14.6416 0.7245 -0.2437 -0.1091 0.9842 -0.4262 -0.5591 0.2627 -0.0122 -0.0626 -0.4104 -0.1535 0.8205 -0.0699 -0.0072 0.6408 -0.0078 0.4592 -10.7374 0.3306 36.8706 10 25.532 23.2095 -2.8346 76.8914 1.7078 22.7746 -0.4711 -0.5546 -0.491 -0.4117 0.3422 0.5451 1.9763 0.1525 0.1288 0.4146 0.0346 0.0196 0.2117 0.0615 0.2256 -7.634 8.7741 39.8615 11 17.8784 -0.069 1.2666 23.2145 0.0638 8.6851 0.1879 0.2089 -0.497 -0.4885 0.0984 0.3455 -0.1113 0.4281 -0.2863 0.337 0.0705 0.0144 0.2121 0.0301 0.0745 -3.3766 15.8683 40.068 12 2.5429 1.1443 5.0193 14.7718 8.4058 7.4046 0.0035 0.1852 0.3233 -0.8225 -0.1668 -0.102 -0.4671 0.0438 0.1633 0.4174 0.0383 0.054 0.2556 0.1113 0.2123 -1.4409 25.2822 42.6262 13 2.3694 -2.8174 1.1597 21.9577 -9.6479 19.3862 -0.1583 0.5118 0.4999 -0.5775 -0.2371 -1.2874 -0.8344 0.8208 0.3954 0.3404 -0.1057 0.0838 0.3109 0.0567 0.3171 5.2643 26.3007 45.1506 14 12.8137 10.9794 -6.7024 15.74 -6.8548 7.9776 0.0613 0.1481 -0.7314 -0.1463 0.0431 0.0755 0.5865 -0.1199 -0.1044 0.3238 0.0455 -0.0419 0.1636 0.0219 0.2182 -2.7223 9.6317 51.5854 15 22.5444 11.0655 6.7718 16.0458 6.493 12.1972 0.059 -0.6258 -1.2724 0.497 -0.1672 -0.1189 0.9128 0.0254 0.1082 0.3314 0.0466 0.0119 0.1039 0.0716 0.2208 -2.4573 12.0396 60.3601 16 13.8639 -1.5139 0.9077 1.4209 0.5112 5.3571 0.1671 0.0184 -0.6182 0.0925 -0.0763 0.0599 0.3995 -0.0349 -0.0908 0.2134 -0.0147 -0.0002 0.0916 0.0202 0.1416 -4.4346 21.5748 57.8844 17 27.9413 -2.8233 -14.0775 21.4742 -3.8521 12.3874 0.2547 -0.2504 -0.5609 -0.522 -0.4377 -1.1244 1.0474 -0.103 0.183 0.465 -0.1202 -0.0108 0.3066 -0.0591 0.4856 -15.0781 15.4587 54.2444 18 9.7369 -2.4929 -1.8489 3.7648 0.3465 2.4179 -0.076 0.1247 -0.4694 0.2567 -0.1854 0.5036 0.3929 -0.2746 0.2614 0.3045 -0.0647 0.0754 0.2097 -0.0061 0.2392 -13.7048 19.4459 65.4314 19 11.991 -7.6965 3.4112 7.8271 -0.5312 9.5604 0.2691 0.3365 -0.1901 -0.2129 -0.2545 0.4509 0.0787 -0.3326 -0.0146 0.1792 -0.0293 0.0375 0.1306 0.0284 0.1458 -8.5203 25.1843 60.3405 20 6.3784 0.4674 -0.63 8.2079 -2.0894 16.3577 0.1076 0.0871 0.2173 0.1823 -0.027 -0.0186 -0.2157 0.3129 -0.0805 0.136 0.0225 0.02 0.1575 -0.0374 0.201 -7.1308 38.3558 67.8903 21 19.0091 6.3085 -13.3866 15.9691 -2.819 20.3758 -0.0346 -1.2389 -0.3295 1.1309 -0.3191 0.1694 0.2183 0.3344 0.3537 0.3073 0.0234 -0.0199 0.222 0.0452 0.1587 -3.2396 28.8855 77.3095 22 0.3143 -0.3788 -4.4751 1.036 -2.9584 19.6637 0.0143 0.1331 0.2454 0.2055 -0.0829 -0.2036 0.0479 0.6805 0.0687 0.2108 0.073 -0.0133 0.3225 -0.0098 0.2391 1.2964 32.785 69.107 23 7.9144 -5.2484 -2.853 24.2803 -0.0576 6.9141 -0.1682 0.3621 0.5154 0.0394 -0.076 -1.0249 -0.4546 0.362 0.2442 0.2552 -0.0097 0.0454 0.3697 0.0111 0.2559 4.4588 35.3943 63.4742 24 17.933 4.7189 -5.4312 7.9895 1.0747 14.5883 0.0142 1.4065 0.2241 -1.5935 0.3826 -1.0147 -0.3942 1.089 -0.3967 0.4982 -0.0909 0.2112 0.5054 -0.0097 0.5287 -0.0013 42.7951 60.8136 25 17.4977 2.8744 -5.9455 5.8923 1.0837 7.658 0.2465 -0.7051 -0.2344 0.6933 -0.3944 0.5658 -0.2563 -0.2959 0.1479 0.1892 0.0042 0.0659 0.158 -0.0278 0.2236 -13.7589 41.1174 75.2045 26 33.4306 18.5938 6.6496 16.0072 7.6268 14.2128 -0.4146 0.5369 0.62 -0.1383 0.7742 -0.3979 0.0942 1.3913 -0.3596 0.2566 0.1095 0.0476 0.4429 -0.1002 0.4269 -32.0199 38.6735 91.5502 27 38.0541 2.93 -24.1924 20.1402 -6.278 35.432 0.1692 -0.8348 0.1896 0.651 0.0026 0.628 0.2384 -1.2087 -0.1718 0.3978 -0.1348 0.0788 0.6414 -0.157 0.3412 -19.8013 43.8151 89.4579 28 39.0876 -3.6198 -20.6623 1.368 -1.5998 19.5398 0.4578 -1.4011 0.3593 0.6261 -0.0503 0.6034 -0.4393 0.4546 -0.4076 0.5348 -0.1883 0.1979 0.3661 -0.2091 0.475 -7.2028 42.9302 82.0184 29 21.8899 2.787 -10.5625 0.553 -2.2942 9.5498 0.3015 -0.49 0.3767 0.1877 -0.2818 0.0932 0.3336 -0.0061 -0.0197 0.4298 -0.1942 -0.0663 0.3076 0.0169 0.2015 0.2129 40.2289 75.4803 30 15.0076 -4.0659 -1.6793 2.8108 -0.991 2.8523 -0.0746 -0.1399 0.1172 0.1142 -0.087 -0.1076 0.1211 0.137 0.1616 0.1898 -0.0439 0.002 0.1688 -0.0094 0.1634 -0.1254 44.823 71.3221 31 13.9459 10.5304 -5.4808 12.7367 -3.3271 5.4299 0.2694 0.0849 0.5056 0.2136 -0.2406 0.8819 -0.1851 -0.4733 -0.0288 0.2056 0.0243 0.0498 0.3086 -0.0853 0.3451 -19.6673 41.5445 75.1842 32 3.269 -3.7317 -3.4134 7.836 2.0768 25.0843 -0.0428 0.3379 -0.0765 -0.2358 -0.2747 1.1309 0.2279 -1.0868 0.3175 0.1317 -0.0215 0.0353 0.2689 -0.0844 0.3883 -20.5044 37.2774 68.5985 33 23.4191 4.8158 -7.9662 8.1776 -2.4419 20.911 -0.1197 0.2929 1.0156 -0.2799 -0.1322 0.8085 -0.8168 -1.1151 0.2518 0.2037 0.0849 -0.0397 0.1891 -0.0052 0.2572 -15.2035 41.6658 62.4117 34 7.8983 -2.526 4.8321 5.4079 0.0968 7.7869 -0.0596 -0.0551 -0.22 0.093 -0.3219 0.0537 0.0727 -0.1131 0.3815 0.1299 -0.0315 0.0286 0.1176 -0.0159 0.1512 -9.1769 33.8384 64.705 35 27.6239 -3.5618 -3.8983 -0.6366 1.1137 0.9411 -0.0463 -0.0975 0.0036 0.3842 -0.1802 0.0241 0.3487 -0.2194 0.2265 0.4258 -0.0605 0.078 0.2621 0.0382 0.2449 -13.5744 27.1541 76.4581 36 11.3598 3.1583 -0.7955 9.0751 2.2745 26.6317 0.1947 -0.8992 0.223 0.5653 -0.25 0.8047 0.7108 -1.191 0.0553 0.2536 -0.1239 0.1756 0.2943 -0.1016 0.3374 -22.6986 27.9526 75.8567 37 10.9079 5.2304 -2.7776 27.4699 -9.4948 18.4563 -0.2124 0.5456 0.0298 -0.4408 0.2576 1.7794 0.7283 -1.1798 -0.0452 0.1172 -0.0453 0.003 0.2879 -0.1066 0.348 -20.6662 27.7589 63.7734 38 4.6289 -3.6223 3.1456 10.3297 -0.8246 4.6568 -0.0642 -0.101 -0.2478 0.3298 0.0724 0.3939 0.0464 -0.1906 -0.0082 0.1336 -0.0207 0.0597 0.1471 0.0022 0.1826 -9.3485 28.5134 65.0411
Refinement TLS group Show large table (5 x 38) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A1 - 5 2 X-RAY DIFFRACTION 2 A6 - 10 3 X-RAY DIFFRACTION 3 A11 - 20 4 X-RAY DIFFRACTION 4 A21 - 25 5 X-RAY DIFFRACTION 5 A26 - 32 6 X-RAY DIFFRACTION 6 A33 - 39 7 X-RAY DIFFRACTION 7 A40 - 44 8 X-RAY DIFFRACTION 8 A45 - 52 9 X-RAY DIFFRACTION 9 A53 - 58 10 X-RAY DIFFRACTION 10 A59 - 63 11 X-RAY DIFFRACTION 11 A64 - 69 12 X-RAY DIFFRACTION 12 A70 - 76 13 X-RAY DIFFRACTION 13 A77 - 83 14 X-RAY DIFFRACTION 14 A84 - 91 15 X-RAY DIFFRACTION 15 A92 - 100 16 X-RAY DIFFRACTION 16 A101 - 111 17 X-RAY DIFFRACTION 17 A112 - 117 18 X-RAY DIFFRACTION 18 A118 - 130 19 X-RAY DIFFRACTION 19 A131 - 138 20 X-RAY DIFFRACTION 20 B1 - 10 21 X-RAY DIFFRACTION 21 B11 - 16 22 X-RAY DIFFRACTION 22 B17 - 22 23 X-RAY DIFFRACTION 23 B23 - 27 24 X-RAY DIFFRACTION 24 B28 - 33 25 X-RAY DIFFRACTION 25 B34 - 40 26 X-RAY DIFFRACTION 26 B44 - 51 27 X-RAY DIFFRACTION 27 B52 - 61 28 X-RAY DIFFRACTION 28 B62 - 70 29 X-RAY DIFFRACTION 29 B71 - 75 30 X-RAY DIFFRACTION 30 B76 - 85 31 X-RAY DIFFRACTION 31 B86 - 91 32 X-RAY DIFFRACTION 32 B92 - 97 33 X-RAY DIFFRACTION 33 B98 - 102 34 X-RAY DIFFRACTION 34 B103 - 108 35 X-RAY DIFFRACTION 35 B109 - 116 36 X-RAY DIFFRACTION 36 B117 - 123 37 X-RAY DIFFRACTION 37 B124 - 130 38 X-RAY DIFFRACTION 38 B131 - 138