Software Name Version Classification HKL-3000data collection SHELXSphasing REFMAC5.2.0019refinement HKL-3000data reduction SCALEPACKdata scaling
Refinement Method to determine structure : MAD / Resolution : 2.3→39.28 Å / Cor.coef. Fo :Fc : 0.952 / Cor.coef. Fo :Fc free : 0.93 / SU B : 14.239 / SU ML : 0.176 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / ESU R : 0.268 / ESU R Free : 0.224 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.254 1884 5.1 % RANDOM Rwork 0.21 - - - obs 0.212 35204 90.5 % -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.2 Å / Solvent model : MASKDisplacement parameters Biso mean : 31.59 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.01 Å2 0 Å2 0 Å2 2- - 0.23 Å2 0 Å2 3- - - -0.24 Å2
Refinement step Cycle : LAST / Resolution : 2.3→39.28 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 4536 0 0 226 4762
Refine LS restraints Show large table (5 x 33) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.014 0.022 4436 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.436 1.956 5980 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg5.423 5 564 X-RAY DIFFRACTION r_dihedral_angle_2_deg40.399 25.667 180 X-RAY DIFFRACTION r_dihedral_angle_3_deg16.389 15 758 X-RAY DIFFRACTION r_dihedral_angle_4_deg20.107 15 6 X-RAY DIFFRACTION r_chiral_restr0.121 0.2 706 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.02 3252 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refined0.225 0.2 2054 X-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refined0.304 0.2 3129 X-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refined0.149 0.2 197 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.146 0.2 45 X-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refined0.207 0.2 7 X-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it0.663 1.5 2867 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it1.138 2 4495 X-RAY DIFFRACTION r_scbond_it2.115 3 1778 X-RAY DIFFRACTION r_scangle_it2.946 4.5 1485 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
Refine LS restraints NCS Dom-ID : 1 / Auth asym-ID : A / Ens-ID : 1 / Refine-ID : X-RAY DIFFRACTION
Number Type Rms dev position (Å)Weight position 1076 tight positional0.05 0.05 1006 loose positional0.44 5 1076 tight thermal0.16 0.5 1006 loose thermal1.78 10
LS refinement shell Resolution : 2.3→2.36 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.318 112 - Rwork 0.267 1948 - obs - - 69.64 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 30) 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 3.0778 -0.9006 -1.8837 30.5353 -8.976 10.4416 -0.1646 0.2482 -0.5276 -1.0011 0.1367 -1.6082 0.0142 0.8077 0.0279 -0.048 0.0096 0.0899 0.2414 -0.0026 0.2376 61.5895 10.4437 29.4135 2 1.9792 0.7848 -0.3641 3.832 -0.3667 1.0968 -0.032 0.3274 -0.1317 -0.3322 -0.0016 -0.0887 0.0835 0.2679 0.0336 0.0184 0.0106 0.0374 0.1308 -0.011 0.0379 52.6068 11.4665 26.1945 3 4.7932 0.9841 -1.2112 2.1825 -0.5311 4.3845 -0.1545 0.0963 0.2145 -0.181 -0.0305 0.0227 -0.1745 -0.2575 0.185 0.0382 0.0002 0.0125 0.0866 -0.0183 0.0616 42.1357 18.855 32.7407 4 4.8474 1.5677 0.392 3.7914 2.6863 8.1638 -0.0359 0.2299 -0.0899 0.0817 -0.0361 0.0471 0.2342 -0.0829 0.072 0.0169 -0.0197 0.0373 0.0377 -0.0139 0.059 36.1705 13.311 40.228 5 11.8509 -0.8874 0.2533 4.2444 -2.1586 1.1012 0.2243 0.7062 0.5463 -0.1949 -0.0908 0.0392 -0.031 0.3674 -0.1335 0.0253 0.0199 0.0264 0.1479 -0.0137 0.0268 32.9203 24.8832 38.3282 6 8.743 -3.9127 -0.5733 17.4303 1.6288 16.5725 -0.2209 0.0053 -0.394 0.3627 0.2551 1.013 0.5068 -0.8273 -0.0342 -0.0063 -0.0805 0.0052 0.2356 -0.0902 0.0702 25.8454 13.4516 40.156 7 9.7303 1.2598 2.6178 0.9995 3.1754 10.3243 -0.1127 0.0525 -0.0865 0.0409 0.0059 0.0402 0.0884 0.0338 0.1068 -0.0371 -0.0401 0.046 0.1131 -0.0177 0.0457 28.4559 20.2204 47.9486 8 1.4802 -0.8778 0.4192 10.3258 -12.2579 22.5716 -0.0814 0.9217 0.055 -0.5452 0.3485 0.6696 0.7586 -1.2459 -0.2671 -0.0183 -0.0642 0.007 0.1532 -0.0155 0.0746 20.6774 14.5751 51.8051 9 9.0269 -7.4552 5.2573 6.1572 -4.3419 3.0619 0.168 0.3636 -0.6605 0.2198 0.0604 0.6338 0.555 -0.3746 -0.2284 0.277 0.0003 0.0547 0.1682 -0.0468 0.2602 23.0371 20.669 57.7358 10 4.8101 -4.2905 3.8392 3.8272 -3.4487 7.2062 0.3665 0.0142 -0.7495 -0.6126 -0.0333 0.4667 1.0109 -0.1095 -0.3332 0.1362 0.0345 -0.0351 0.0282 -0.0098 0.0702 10.6228 19.8141 55.3991 11 15.1182 12.7672 2.4522 17.0643 9.3338 8.7941 0.5352 -0.4861 0.278 -0.2674 -0.2491 0.346 1.2976 0.6001 -0.2861 0.4274 -0.0458 0.2046 -0.1463 0.0202 0.0826 19.152 9.4185 67.2366 12 2.669 -1.0479 2.6395 2.7097 -1.5643 4.9914 0.2833 0.2635 -0.652 -0.1676 0.1152 0.0663 0.5825 -0.2537 -0.3985 0.0717 -0.0587 -0.0289 0.0242 0.0047 0.0805 14.398 15.5986 69.6586 13 1.1445 -2.6454 1.2372 7.3533 -6.0798 9.9284 0.0711 -0.3346 0.0867 0.0386 0.1049 -0.0563 0.1121 -0.2563 -0.1761 0.0319 -0.0038 0.0119 0.0604 -0.0085 0.0678 6.1084 23.3029 69.2851 14 9.1501 -0.8513 0.8252 6.4163 -2.5686 7.5138 0.1066 -1.1936 -0.8442 -0.1401 0.4845 0.9901 0.8872 -1.1539 -0.5911 -0.1121 -0.1479 -0.0112 0.2511 0.1145 0.0268 0.3085 15.7138 72.5422 15 46.1123 -24.139 -8.4275 17.8957 -4.591 16.9504 -0.9598 -1.9469 0.078 0.6596 1.7588 -1.111 -0.1559 -1.0534 -0.799 0.0726 -0.0617 0.1243 0.6121 -0.0898 -0.1699 4.7891 23.1461 79.9562 16 9.4778 6.0219 16.3851 75.3716 13.4715 28.4572 0.6975 -1.7174 -0.6785 2.6251 0.1097 1.1728 0.9704 -0.9059 -0.8072 0.1279 -0.4535 0.2298 0.9155 -0.0312 0.181 1.2155 4.1086 97.9427 17 14.3225 -0.0217 -5.0692 1.865 -5.8191 19.9987 0.5292 -0.5226 0.4747 0.5266 0.0458 0.8035 -0.2259 -0.8826 -0.5749 0.0376 -0.2412 0.1061 0.6068 -0.0496 -0.0303 -0.923 12.5943 104.0806 18 1.4173 -0.1298 0.7386 4.3248 -0.1982 3.6192 -0.0424 -0.4253 -0.3129 0.1218 0.0637 0.0488 0.6341 -0.9989 -0.0214 0.0124 -0.1637 0.0452 0.3843 0.0276 0.0153 9.9467 10.5304 102.0486 19 5.6789 -1.8277 -1.8163 6.2483 -0.0675 7.7714 -0.109 -0.2318 0.1156 0.1754 -0.0313 0.0073 0.0243 -0.2375 0.1404 -0.0021 -0.0167 0.0306 0.2788 -0.0057 0.0617 17.5186 17.8312 94.5935 20 2.2357 -0.783 -0.0102 0.9596 1.5171 8.5045 -0.0462 -0.3065 0.1205 0.1305 0.0075 -0.1413 0.553 0.0723 0.0387 0.0211 0.0054 0.0357 0.1748 0.0337 0.06 24.9282 14.4909 92.4377 21 5.3609 -2.8871 0.9301 5.4557 -1.9144 4.3008 0.0791 0.1325 0.219 -0.0378 -0.0715 -0.3385 -0.0129 0.7099 -0.0076 0.0596 -0.0122 0.0017 0.2753 -0.0246 0.044 31.108 21.0588 91.0589 22 8.8286 -2.6375 1.4146 2.597 -3.0326 13.1262 -0.1309 -0.2674 -0.2616 -0.1254 0.1535 -0.0608 0.4906 0.4009 -0.0226 -0.0274 0.0496 0.0522 0.162 0.0036 0.0545 33.1616 18.8696 81.6855 23 1.0588 1.2291 -0.7938 1.4266 -0.9214 0.5951 0.4238 -0.6512 -0.4699 0.0462 -0.1591 -0.3799 0.2081 0.9246 -0.2647 0.2171 0.0101 -0.0218 0.385 0.0081 0.2347 40.3263 18.8567 74.6296 24 0.9307 0.3555 -2.576 6.2927 0.6799 7.5795 0.0921 0.1509 -0.7496 0.541 0.0826 -0.4701 1.0893 0.5007 -0.1747 0.0777 0.0398 -0.0317 0.1958 -0.0112 0.0226 50.2637 17.905 71.5839 25 0.3902 1.009 1.0799 2.7715 2.4889 3.5562 0.1032 -0.3672 -0.3321 0.3975 -0.0877 0.099 0.6185 0.1931 -0.0155 0.1012 0.0594 -0.0067 0.1999 0.0407 0.0793 44.7479 16.911 62.478 26 16.2321 7.6762 6.1443 3.6939 3.6023 9.9419 0.3064 0.5692 -0.2335 0.3457 0.0956 0.1147 0.5842 0.7771 -0.4021 0.1186 0.1278 0.0257 0.2372 -0.0297 0.0483 50.6765 15.1524 55.0415 27 13.7856 6.7803 1.6829 7.2539 5.4011 5.5424 0.2205 0.1463 -0.1219 0.1349 0.3482 -0.307 0.1607 0.5556 -0.5688 -0.0086 -0.0378 -0.014 0.2866 -0.0462 0.0011 59.602 26.1645 64.3207 28 5.7046 4.9412 1.7306 8.2882 5.1442 3.8401 -0.1143 1.0109 -0.9788 0.5248 1.0249 -1.2566 0.9769 2.3989 -0.9106 -0.0538 0.2111 -0.0796 0.3852 -0.2087 0.1765 62.1096 15.1259 58.0974 29 7.3232 4.4244 7.0905 53.8443 -15.5309 14.5381 -0.0705 1.9345 -0.6163 -2.1107 -0.2029 0.0853 0.6739 -1.3662 0.2734 0.2973 0.0014 0.1282 0.7085 -0.0918 -0.081 56.7243 16.0689 46.598 30 78.2556 25.6046 4.2154 19.9561 23.7303 43.3734 -1.5018 0.5497 2.8893 -1.7347 2.4078 1.3235 -1.7173 0.2871 -0.9061 0.032 -0.0839 0.0823 0.6022 0.1147 0.0035 56.6438 26.1644 49.3482
Refinement TLS group Show large table (5 x 30) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A0 - 11 2 X-RAY DIFFRACTION 2 A12 - 61 3 X-RAY DIFFRACTION 3 A62 - 87 4 X-RAY DIFFRACTION 4 A88 - 107 5 X-RAY DIFFRACTION 5 A108 - 118 6 X-RAY DIFFRACTION 6 A119 - 128 7 X-RAY DIFFRACTION 7 A129 - 154 8 X-RAY DIFFRACTION 8 A155 - 168 9 X-RAY DIFFRACTION 9 A169 - 185 10 X-RAY DIFFRACTION 10 A186 - 197 11 X-RAY DIFFRACTION 11 A198 - 204 12 X-RAY DIFFRACTION 12 A205 - 236 13 X-RAY DIFFRACTION 13 A237 - 252 14 X-RAY DIFFRACTION 14 A253 - 275 15 X-RAY DIFFRACTION 15 A276 - 282 16 X-RAY DIFFRACTION 16 B0 - 5 17 X-RAY DIFFRACTION 17 B6 - 17 18 X-RAY DIFFRACTION 18 B18 - 61 19 X-RAY DIFFRACTION 19 B62 - 80 20 X-RAY DIFFRACTION 20 B81 - 107 21 X-RAY DIFFRACTION 21 B108 - 125 22 X-RAY DIFFRACTION 22 B126 - 154 23 X-RAY DIFFRACTION 23 B155 - 188 24 X-RAY DIFFRACTION 24 B189 - 198 25 X-RAY DIFFRACTION 25 B199 - 224 26 X-RAY DIFFRACTION 26 B225 - 243 27 X-RAY DIFFRACTION 27 B244 - 256 28 X-RAY DIFFRACTION 28 B257 - 269 29 X-RAY DIFFRACTION 29 B270 - 276 30 X-RAY DIFFRACTION 30 B277 - 282