Software Name Version Classification NB DENZOdata reductionShow SCALEPACKdata scalingShow REFMAC5.2.0019refinementShow PDB_EXTRACT3.006 data extractionShow SBC-Collectdata collection HKL-3000data reduction SHELXDphasing MLPHAREphasing DMphasing SOLVEphasing RESOLVEphasing HKL-3000phasing
Refinement Method to determine structure : SAD / Resolution : 1.8→44.8 Å / Cor.coef. Fo :Fc : 0.967 / Cor.coef. Fo :Fc free : 0.963 / Occupancy max : 1 / Occupancy min : 0.35 / SU B : 4.918 / SU ML : 0.077 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / σ(I) : 0 / ESU R : 0.123 / ESU R Free : 0.107 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.19 1549 5 % RANDOM Rwork 0.172 - - - all 0.173 30799 - - obs 0.173 30799 98.61 % -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.2 Å / Solvent model : MASKDisplacement parameters Biso max : 58.77 Å2 / Biso mean : 31.352 Å2 / Biso min : 20.56 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.03 Å2 0 Å2 0 Å2 2- - 1.21 Å2 0 Å2 3- - - -1.23 Å2
Refinement step Cycle : LAST / Resolution : 1.8→44.8 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 2475 0 14 199 2688
Refine LS restraints Show large table (5 x 17) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.017 0.022 2612 X-RAY DIFFRACTION r_angle_refined_deg1.607 1.942 3522 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.331 5 312 X-RAY DIFFRACTION r_dihedral_angle_2_deg33.653 24.014 142 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.695 15 491 X-RAY DIFFRACTION r_dihedral_angle_4_deg19.587 15 17 X-RAY DIFFRACTION r_chiral_restr0.119 0.2 376 X-RAY DIFFRACTION r_gen_planes_refined0.007 0.02 1981 X-RAY DIFFRACTION r_nbd_refined0.204 0.2 1189 X-RAY DIFFRACTION r_nbtor_refined0.31 0.2 1797 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.142 0.2 163 X-RAY DIFFRACTION r_symmetry_vdw_refined0.347 0.2 23 X-RAY DIFFRACTION r_symmetry_hbond_refined0.174 0.2 12 X-RAY DIFFRACTION r_mcbond_it0.967 1.5 1553 X-RAY DIFFRACTION r_mcangle_it1.492 2 2423 X-RAY DIFFRACTION r_scbond_it2.559 3 1216 X-RAY DIFFRACTION r_scangle_it3.805 4.5 1089
LS refinement shell Resolution : 1.799→1.846 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.292 84 - Rwork 0.24 1873 - all - 1957 - obs - 1957 86.33 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 20) 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 4.8006 4.3605 -3.3426 4.727 -5.9425 13.3505 -0.0432 0.1365 0.2961 -0.0129 0.1258 0.5176 -0.2882 -0.4722 -0.0826 -0.1098 -0.0382 -0.0191 0.044 0.0153 -0.043 2.8614 76.8081 11.1426 2 0.8751 -0.5371 -0.9314 3.5897 0.5944 3.9711 -0.0099 -0.0921 0.1467 0.0868 0.1248 0.4373 -0.3937 -0.0761 -0.115 -0.1253 0.0746 0.0117 0.0049 0.0335 -0.0401 3.2532 86.8325 12.4337 3 6.6846 2.1298 4.1673 1.787 0.1452 3.8596 -0.159 0.3223 0.4338 -0.1006 0.0646 -0.074 -0.2434 -0.0392 0.0943 -0.0313 0.0204 -0.0222 -0.0103 0.0589 -0.1026 17.7419 91.6713 -4.0639 4 0.9728 0.2143 0.2473 0.0557 0.1478 1.0867 -0.0159 0.16 0.113 -0.0538 0.0093 0.0093 -0.0156 -0.0639 0.0066 -0.0628 0.0039 -0.0077 -0.0626 0.0097 -0.0573 20.1143 86.9775 3.2447 5 1.7978 -0.5222 -2.376 2.0211 -0.4946 4.4166 0.1788 -0.291 -0.0052 -0.158 -0.1969 -0.1889 -0.0569 0.3215 0.0182 -0.0354 0.0115 0.0101 -0.0585 0.0252 -0.0803 25.2637 81.7073 -0.5398 6 1.4228 -0.6056 -1.4734 1.3914 1.1214 3.8856 -0.0636 -0.1068 0.0343 0.0518 0.0213 -0.1452 0.0098 0.181 0.0423 -0.0641 -0.0087 -0.0231 -0.078 0.0058 -0.0546 25.85 87.8668 10.2585 7 1.415 0.0928 -0.2142 0.445 -1.3621 4.1731 0.0949 0.146 0.1101 0.0204 0.0784 -0.0011 -0.1444 -0.2199 -0.1733 -0.0669 0.0205 -0.0147 -0.0662 0.0116 -0.0894 14.1995 87.4619 3.0118 8 1.7458 1.1357 -0.7504 7.0926 -1.6716 1.9145 0.0395 -0.1365 0.0754 0.2181 0.0264 0.1595 -0.2402 -0.3041 -0.066 -0.062 0.0467 0.006 -0.0006 -0.0136 -0.092 9.9262 82.9384 20.465 9 0.0343 -0.0721 0.1188 0.1513 -0.2496 0.4116 -0.11 0.0843 0.1071 -0.0348 0.0992 -0.0128 0.1315 -0.0522 0.0109 -0.0374 -0.0002 -0.0035 -0.0351 -0.006 -0.0802 21.1425 71.9279 10.5482 10 74.2221 32.7587 0.2181 14.8934 -4.7155 53.2299 1.3748 1.7978 -2.7946 -1.2225 -0.4926 -0.7762 0.7518 -1.2085 -0.8822 0.3997 0.1081 -0.0883 0.5033 -0.0315 0.2128 33.0578 66.9872 -1.6532 11 8.1551 -2.0425 -2.4137 8.6366 1.5417 4.2339 -0.1247 -0.3791 -0.336 0.7001 0.1053 -0.4267 0.3404 0.1537 0.0194 0.0066 -0.0393 -0.019 -0.0072 -0.0109 -0.0846 25.2214 71.967 33.6561 12 2.0279 -2.7877 0.5819 15.563 0.3052 0.2711 0.0419 -0.1645 0.0201 0.0617 0.1009 -0.2147 0.1541 -0.4297 -0.1428 0.0342 0.0016 0.0486 -0.0272 -0.0011 -0.1452 16.6671 68.8482 36.5344 13 9.5376 -3.1258 -2.0074 2.7576 -0.4657 2.8384 -0.2526 -0.2891 -0.1736 0.0688 -0.0422 -0.2319 0.2194 0.1278 0.2947 -0.0556 0.0073 0.0044 -0.0901 0.0458 -0.0386 31.0964 59.4992 29.0825 14 11.4831 3.1212 8.8953 3.2756 3.0814 8.9614 0.1781 -0.2114 -0.5459 -0.1035 -0.1049 -0.3049 0.3986 0.2095 -0.0733 -0.0886 0.05 0.0431 -0.0876 0.0261 -0.006 36.4817 56.9765 16.3553 15 1.046 0.1962 -0.8771 0.4032 -0.0079 2.0915 0.0253 -0.051 -0.1236 -0.0434 -0.0734 -0.1329 0.0773 0.1617 0.0481 -0.073 0.0194 0.0275 -0.059 0.0106 -0.049 35.2954 64.3184 14.1116 16 2.1482 0.8305 -0.3605 1.8662 1.099 2.5802 -0.0095 0.1113 -0.0119 -0.2272 -0.1654 0.0133 -0.0732 -0.0967 0.175 -0.0534 0.0018 0.0059 -0.0793 -0.0001 -0.0795 28.3326 63.8154 15.1914 17 8.2149 0.5879 0.2007 0.043 -0.0234 1.6185 -0.069 -0.0287 -0.055 0.0282 -0.0326 -0.0649 0.1313 -0.0502 0.1016 -0.0724 -0.016 -0.0036 -0.0914 0.032 -0.0572 26.44 62.0915 24.6371 18 6.3032 -3.9587 -1.4404 10.7256 7.312 5.3119 -0.1173 -0.1014 -0.4646 0.7676 -0.1468 0.4876 0.4796 -0.2221 0.2641 -0.0608 -0.0756 0.0461 0.0428 0.032 -0.0709 12.2165 64.9059 27.427 19 0.913 0.4483 -0.2725 0.5348 -0.5744 0.9968 -0.0701 -0.0837 -0.0005 -0.008 -0.0495 -0.0571 0.0212 -0.0161 0.1196 -0.0571 0.0137 -0.0081 -0.0675 0.0131 -0.0627 22.2492 76.0932 18.5457 20 28.4149 -0.1243 -7.5577 13.3913 -9.9557 27.8729 -0.2987 0.6194 0.4052 -0.7578 0.18 -1.5409 -0.4388 1.9046 0.1187 0.053 -0.0409 0.0214 0.1889 0.0747 0.1622 35.8071 79.8591 3.9307
Refinement TLS group Show large table (7 x 20) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA1 - 16 4 - 19 2 X-RAY DIFFRACTION 2 AA17 - 30 20 - 33 3 X-RAY DIFFRACTION 3 AA31 - 40 34 - 43 4 X-RAY DIFFRACTION 4 AA41 - 60 44 - 63 5 X-RAY DIFFRACTION 5 AA61 - 79 64 - 82 6 X-RAY DIFFRACTION 6 AA80 - 95 83 - 98 7 X-RAY DIFFRACTION 7 AA96 - 109 99 - 112 8 X-RAY DIFFRACTION 8 AA110 - 123 113 - 126 9 X-RAY DIFFRACTION 9 AA124 - 141 127 - 144 10 X-RAY DIFFRACTION 10 AA142 - 146 145 - 149 11 X-RAY DIFFRACTION 11 BB-2 - 13 1 - 16 12 X-RAY DIFFRACTION 12 BB14 - 25 17 - 28 13 X-RAY DIFFRACTION 13 BB26 - 33 29 - 36 14 X-RAY DIFFRACTION 14 BB34 - 43 37 - 46 15 X-RAY DIFFRACTION 15 BB44 - 74 47 - 77 16 X-RAY DIFFRACTION 16 BB75 - 98 78 - 101 17 X-RAY DIFFRACTION 17 BB99 - 112 102 - 115 18 X-RAY DIFFRACTION 18 BB113 - 118 116 - 121 19 X-RAY DIFFRACTION 19 BB119 - 139 122 - 142 20 X-RAY DIFFRACTION 20 BB140 - 145 143 - 148