Software Name Version Classification PHENIX(2.0_5904: ???)refinement Aimlessdata scaling XDSdata reduction PHASERphasing PDB_EXTRACTdata extraction
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.85→45.05 Å / SU ML : 0.44 / Cross valid method : FREE R-VALUE / σ(F) : 1.34 / Phase error : 30.55 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2586 2822 5.13 % Rwork 0.1945 - - obs 0.1977 54983 99.53 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 2.85→45.05 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 13001 0 384 27 13412
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.004 13529 X-RAY DIFFRACTION f_angle_d0.697 18448 X-RAY DIFFRACTION f_dihedral_angle_d18.18 4664 X-RAY DIFFRACTION f_chiral_restr0.046 2164 X-RAY DIFFRACTION f_plane_restr0.005 2391
LS refinement shell Show large table (7 x 20) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.85-2.9 0.4655 113 0.4274 2617 X-RAY DIFFRACTION 99 2.9-2.95 0.4026 161 0.3638 2550 X-RAY DIFFRACTION 99 2.95-3.01 0.3646 158 0.3134 2591 X-RAY DIFFRACTION 99 3.01-3.07 0.354 136 0.296 2592 X-RAY DIFFRACTION 99 3.07-3.14 0.3655 155 0.2855 2606 X-RAY DIFFRACTION 99 3.14-3.21 0.3492 154 0.2684 2537 X-RAY DIFFRACTION 99 3.21-3.29 0.3063 148 0.251 2578 X-RAY DIFFRACTION 99 3.29-3.38 0.2895 142 0.241 2617 X-RAY DIFFRACTION 99 3.38-3.48 0.3213 138 0.2482 2615 X-RAY DIFFRACTION 100 3.48-3.59 0.327 145 0.2376 2563 X-RAY DIFFRACTION 100 3.59-3.72 0.2623 145 0.1967 2614 X-RAY DIFFRACTION 100 3.72-3.87 0.227 142 0.177 2619 X-RAY DIFFRACTION 100 3.87-4.04 0.2502 132 0.1701 2633 X-RAY DIFFRACTION 100 4.04-4.26 0.2257 148 0.1633 2597 X-RAY DIFFRACTION 100 4.26-4.52 0.2059 150 0.1492 2592 X-RAY DIFFRACTION 100 4.52-4.87 0.2168 128 0.1447 2620 X-RAY DIFFRACTION 100 4.87-5.36 0.2164 115 0.1603 2663 X-RAY DIFFRACTION 100 5.36-6.13 0.2871 142 0.1879 2623 X-RAY DIFFRACTION 100 6.14-7.72 0.2225 133 0.1774 2657 X-RAY DIFFRACTION 100 7.72-45.05 0.2019 137 0.1612 2677 X-RAY DIFFRACTION 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 35) 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 5.6725 -1.1217 1.3853 1.804 -0.547 2.6597 -0.8871 -0.1904 0.3493 0.7385 0.4061 -0.0371 -0.5589 -0.1492 0.5241 0.6721 0.1059 -0.08 0.425 0.059 0.4926 64.8607 1.3367 36.7166 2 2.5216 -0.7219 0.0421 2.6348 -1.242 0.6675 -0.0013 0.2075 -0.1065 0.1435 0.0121 -0.0449 -0.2101 0.1707 0.0453 0.6928 0.0463 -0.1957 0.6639 -0.0398 0.6908 70.748 -2.318 37.8096 3 5.0671 0.35 -0.0484 3.6031 -0.0414 3.257 0.3009 -0.8373 -0.3445 0.4525 -0.286 0.0981 -0.2199 0.0767 -0.1143 0.7326 0.2062 -0.0611 0.9272 -0.0575 0.5625 62.5118 0.7728 45.8833 4 5.8918 -2.1194 1.2876 3.8177 -1.1724 2.2343 0.1464 0.1669 -0.461 0.1348 -0.0343 -0.0047 -0.0157 0.0679 -0.1402 0.7232 0.0172 -0.1124 0.6726 0.0292 0.506 62.1475 -5.2566 35.4323 5 5.534 1.219 0.2917 2.2113 -0.8155 1.7664 -0.4274 -0.3219 0.2498 -0.4405 0.378 0.3402 0.1004 -0.2825 0.0816 0.7032 0.0475 -0.2207 0.5099 0.0885 0.7768 52.8213 0.9076 26.7611 6 0.3681 -0.0222 0.7605 4.062 0.4054 4.5339 0.0723 0.442 -0.0496 -0.0791 -0.053 -0.0821 0.084 0.4697 -0.0003 0.6633 0.0551 -0.1166 0.6176 -0.0452 0.6461 59.6213 0.6936 13.7822 7 5.0924 0.6474 0.3567 4.2571 1.2265 3.9743 -0.3333 -0.0667 -0.3853 0.0511 0.2374 -0.7493 -0.3492 0.6978 -0.26 0.5021 -0.0059 0.0167 0.5788 0.0119 0.6816 70.5444 10.03 16.1897 8 7.8158 -2.6534 -0.1881 1.4842 0.8118 0.995 -0.3607 -0.8634 1.0082 0.0278 0.4821 -0.7501 -0.2887 0.1273 -0.0413 0.7181 0.036 -0.1538 0.5906 0.0626 0.8107 65.2886 14.5874 24.0664 9 5.7423 -3.4164 3.4802 8.6176 -1.6212 7.9716 -0.4761 -0.7048 0.8822 0.002 -0.1365 -0.3635 -0.3089 -0.225 0.5477 0.8014 0.1221 -0.2285 0.8205 0.0562 0.9924 74.5883 16.802 30.1054 10 7.1349 2.4088 1.0524 2.7775 0.0152 3.0226 -0.6272 0.4764 -0.3457 -0.5671 0.4776 -0.6237 0.1665 -0.0209 0.2691 0.7682 -0.033 -0.2882 0.5368 -0.063 0.576 27.2646 -1.4755 -2.4135 11 3.7197 0.256 0.0003 1.3378 -0.5245 1.2906 -0.1854 0.5501 -0.4159 0.0655 0.2085 -0.0579 -0.0807 -0.1463 0.019 0.7899 -0.016 -0.2147 0.6905 0.0014 0.8575 24.6203 -3.7459 -7.1028 12 3.6241 1.5051 2.0081 1.7357 -0.1327 2.8653 0.4301 0.0301 -0.6064 0.3151 -0.0999 -0.3796 0.1914 -0.1442 -0.1699 0.8099 0.0178 -0.1907 0.4972 0.0024 0.7588 34.54 -4.268 3.7271 13 3.1616 -0.8659 0.4282 3.6611 -1.3801 5.6665 -0.05 -0.4797 -0.5294 0.1286 0.4006 0.4802 0.0663 -0.7506 -0.231 0.4986 0.0029 -0.0704 0.5121 0.106 0.6136 28.1689 7.9331 15.2824 14 6.8195 2.4424 -0.0404 2.0673 -2.2373 4.148 -0.0474 0.7009 0.0184 -1.0155 0.8437 1.1188 0.3522 -0.7621 -0.7231 1.0403 -0.128 -0.2766 0.7572 0.1225 0.9453 18.0883 14.9148 0.7074 15 4.2129 1.4009 1.885 2.482 2.7883 3.1291 0.1897 -0.3745 -0.6405 0.4274 0.1144 -0.3691 0.0119 0.0369 -0.1258 0.9081 -0.0784 -0.2762 0.5724 -0.0357 0.9623 14.1672 -19.0176 -11.4676 16 1.2452 0.1147 -0.7736 2.6421 1.2968 3.5898 0.0047 -0.0312 0.0283 0.0548 -0.1839 -0.4731 -0.7265 0.3195 0.3712 0.8109 -0.1372 -0.2892 0.786 0.0749 0.9958 11.2006 -16.2279 -18.5192 17 4.4959 0.9119 2.1129 3.5894 1.161 3.4129 -0.3401 -0.2997 0.5491 0.1101 -0.2094 0.5668 -0.5101 -0.3595 0.5084 0.7131 -0.0206 -0.1347 0.6226 -0.127 0.7979 -4.3145 -20.5024 -24.0367 18 6.8094 -0.6738 0.7006 2.7337 -0.126 2.5 -0.0863 -0.7075 -0.3302 0.2609 0.1137 -0.0344 0.0956 0.2694 0.0505 0.5989 0.0095 -0.0114 0.6702 0.0408 0.4274 4.619 -38.2272 -22.9117 19 2.6451 -0.3601 2.5505 1.2144 -1.3812 3.3803 -0.2125 -0.3501 0.1635 0.25 -0.0934 0.0255 -0.2072 -0.2139 0.3552 0.6685 0.1632 -0.0357 0.7697 -0.0226 0.643 80.8695 -15.7072 53.3804 20 4.8935 -0.781 0.764 5.997 -0.921 1.7601 0.0214 0.752 -0.408 -0.1855 0.0689 -0.444 0.0212 -0.4806 -0.0797 0.6176 0.0371 -0.0175 0.7946 0.0172 0.6151 96.92 -29.8031 53.4104 21 4.9828 -0.3763 1.3657 3.4805 0.7329 1.1712 0.0853 0.0835 -1.0719 -0.082 0.0609 0.8306 0.2221 -0.6628 -0.2576 0.6701 -0.0791 -0.0048 0.9323 -0.0146 0.8498 83.9862 -38.4593 57.1558 22 5.6296 -0.4528 0.7421 2.8943 2.2589 2.2421 0.4869 -0.1131 -0.4489 0.2623 0.2817 0.4871 -0.4799 -0.7536 -0.1144 1.1318 -0.0834 -0.0991 1.3076 0.09 1.1612 72.0517 -33.4702 58.9348 23 4.3435 0.758 0.6426 0.2247 0.2959 1.2913 -0.2252 0.0043 1.175 0.0305 0.037 0.0134 -0.3461 0.0024 0.1738 0.6444 0.0855 0.0437 0.6104 -0.0265 1.0219 49.0175 -32.1349 27.9715 24 4.7072 1.1253 -1.0088 0.9262 -0.3875 2.9056 -0.2777 0.0812 -0.9541 0.1387 0.2264 -0.2442 0.4158 0.3203 0.0028 0.6514 0.0602 -0.1038 0.7782 -0.1028 0.9975 40.3837 -42.8096 31.2504 25 3.2542 1.1875 -0.0121 3.3175 -0.6087 1.9546 -0.1524 0.7263 -0.7999 0.0389 0.3004 -0.7397 0.3136 0.0211 0.0564 0.5795 0.1356 0.0475 0.8515 -0.159 0.9858 44.8336 -39.815 24.9289 26 3.2369 -1.2171 -1.6408 3.1329 0.2086 6.786 0.1051 0.9385 -0.9092 -0.4795 -0.2429 0.1385 0.1915 -0.6657 -0.1046 0.5971 -0.0398 -0.1036 0.6611 -0.0817 0.9542 26.6967 -42.8563 25.2232 27 3.1061 0.4151 0.6785 0.7311 0.8833 4.0968 -0.1041 0.4356 0.0105 0.0422 -0.1683 -0.5185 -0.4296 0.0233 0.1194 0.6547 0.0587 0.0801 0.6955 0.0509 0.8097 24.6746 -33.7587 24.6065 28 4.8507 -2.2668 -0.5712 2.7402 -0.1619 2.9654 0.2597 0.0958 0.4669 -0.0087 -0.4835 -0.1132 -0.4685 0.0933 0.1058 0.7282 -0.0154 -0.1088 0.5548 0.0362 0.7929 24.106 -22.8056 33.9496 29 3.8947 -0.6896 1.2228 2.2039 -0.6543 2.8773 -0.2917 -0.1763 -0.027 0.2042 0.1589 -0.6514 -0.4411 0.3829 0.1766 0.6047 -0.0465 -0.1229 0.6148 -0.0341 0.7684 30.5046 -31.4369 45.171 30 7.3523 1.3555 0.8531 6.6828 -0.9054 3.236 0.0118 -0.2796 -0.7555 -0.3245 0.3436 -0.381 0.1765 0.3153 -0.3941 0.6899 -0.0247 -0.0657 0.6832 -0.0222 0.9898 39.539 -38.9351 49.0783 31 5.3758 0.1043 0.461 0.1874 0.5932 1.7681 -0.0871 0.4575 1.0702 -0.0343 -0.0942 -0.1501 -0.1488 -0.4422 0.1867 0.6937 -0.0111 0.0448 0.593 -0.0468 0.672 60.1283 -34.1814 17.9191 32 2.4041 0.1829 -0.6742 1.7978 -0.9833 5.2065 0.0363 0.0015 -0.0092 -0.3207 0.2259 0.2293 0.4652 -0.5911 -0.2246 0.5748 -0.1027 -0.05 0.5028 -0.0471 0.8823 72.3168 -43.9067 16.116 33 3.7565 -1.0009 -0.0261 0.9746 0.0184 2.6509 0.1347 -0.41 -0.54 0.0047 0.0435 0.2507 0.2072 0.0529 -0.1703 0.5986 -0.08 0.0081 0.4864 -0.0332 0.74 74.0081 -38.244 21.7499 34 2.3712 0.428 0.8943 2.0647 0.3829 3.2183 -0.1603 0.227 0.283 -0.331 0.0384 0.5776 -0.4787 -0.0484 0.141 0.6035 -0.0355 -0.0984 0.4941 -0.0227 0.7441 81.6492 -28.5049 5.2721 35 8.4245 0.359 -5.4039 5.2634 -1.9313 9.643 0.0864 0.5547 -0.1375 0.2364 0.4605 0.3773 0.2472 -1.022 -0.6939 0.8228 -0.0121 -0.0866 0.7454 -0.0501 1.0499 69.1007 -40.6919 -1.8583
Refinement TLS group Show large table (4 x 35) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 7 through 24 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 25 through 70 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 71 through 99 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 100 through 136 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 137 through 177 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 178 through 228 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 229 through 257 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 258 through 292 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 293 through 312 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 8 through 24 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 25 through 98 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 99 through 179 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 180 through 291 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 292 through 311 )15 X-RAY DIFFRACTION 15 chain 'C' and (resid 7 through 45 )16 X-RAY DIFFRACTION 16 chain 'C'