Software Name Version Classification REFMAC5.3.0037refinement MAR345data collection DENZOdata reduction SCALEPACKdata scaling REFMACphasing
Refinement Method to determine structure : FOURIER SYNTHESISStarting model : PDB ENTRY 1R5DResolution : 1.6→27.6 Å / Cor.coef. Fo :Fc : 0.958 / Cor.coef. Fo :Fc free : 0.943 / SU B : 3.041 / SU ML : 0.056 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.095 / ESU R Free : 0.092 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.20363 1575 5.1 % RANDOM Rwork 0.17667 - - - obs 0.17809 29510 97.64 % - all - 31120 - -
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 : 13.69 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.03 Å2 0 Å2 0 Å2 2- - -0.2 Å2 0 Å2 3- - - 0.17 Å2
Refine analyze Luzzati coordinate error obs : 0.197 ÅRefinement step Cycle : LAST / Resolution : 1.6→27.6 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 1882 0 42 309 2233
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_d0.007 0.022 1972 X-RAY DIFFRACTION r_angle_refined_deg1.342 1.971 2661 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.542 5 246 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.209 24.865 74 X-RAY DIFFRACTION r_dihedral_angle_3_deg11.618 15 365 X-RAY DIFFRACTION r_dihedral_angle_4_deg8.804 15 8 X-RAY DIFFRACTION r_chiral_restr0.09 0.2 295 X-RAY DIFFRACTION r_gen_planes_refined0.003 0.02 1420 X-RAY DIFFRACTION r_nbd_refined0.187 0.2 940 X-RAY DIFFRACTION r_nbtor_refined0.289 0.2 1349 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.117 0.2 242 X-RAY DIFFRACTION r_symmetry_vdw_refined0.15 0.2 62 X-RAY DIFFRACTION r_symmetry_hbond_refined0.11 0.2 35 X-RAY DIFFRACTION r_mcbond_it0.512 1.5 1275 X-RAY DIFFRACTION r_mcangle_it0.895 2 2013 X-RAY DIFFRACTION r_scbond_it1.485 3 775 X-RAY DIFFRACTION r_scangle_it2.394 4.5 648
LS refinement shell Resolution : 1.597→1.638 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.25 95 - Rwork 0.193 1863 - obs - - 85.61 %
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 5.6273 0.3354 -1.7783 2.2686 0.6301 6.8477 0.1049 -0.4449 -0.0008 0.2967 -0.1246 -0.0855 0.0777 0.3938 0.0197 0.0476 -0.0312 -0.0059 0.0648 0.0011 -0.0067 11.11 19.4628 23.2601 2 6.2776 -2.6229 0.9468 7.4824 -3.8659 3.7598 0.2164 0.4075 0.3185 -0.4804 -0.0999 0.0535 0.1247 0.0244 -0.1165 0.049 0.0052 -0.0019 0.043 0.0031 0.0203 7.0092 22.6078 9.518 3 3.3837 1.0092 -0.0998 1.9527 -0.7547 2.1474 0.03 0.1027 0.0731 -0.1485 0.0244 0.2625 0.0783 -0.1692 -0.0544 0.0033 -0.0068 -0.0055 0.0178 -0.0071 0.0515 18.683 27.345 5.475 4 14.4668 -6.0402 -7.1881 10.2616 12.4493 15.1052 0.1109 -0.9287 0.195 1.0315 -0.0782 0.042 0.1596 -0.1091 -0.0327 0.0789 -0.0166 0.0154 0.1017 -0.0333 -0.035 23.8376 32.0735 16.7223 5 2.6859 0.383 -0.7074 1.2172 0.258 1.2722 0.0264 0.0554 0.0107 -0.0435 -0.0038 -0.0156 -0.0402 -0.0082 -0.0226 0.0572 0.0029 -0.0131 0.0228 -0.0032 0.0452 34.6896 31.4998 1.2953 6 0.7861 0.489 0.1871 5.3067 4.5374 7.4397 0.0745 0.0077 -0.01 -0.2051 0.1082 -0.1759 -0.349 0.0002 -0.1827 0.0618 -0.0209 0.009 0.0063 0.0053 0.033 42.5822 42.747 2.5107 7 9.8052 1.427 -3.5671 3.2679 -0.9192 4.6238 -0.0617 0.4148 0.0155 -0.2731 0.1443 -0.007 0.1936 0.1059 -0.0826 0.0811 0.0025 -0.0285 0.0523 -0.0004 0.0249 31.8979 33.5222 -5.6141 8 4.0505 -0.5556 -1.3197 1.4793 -2.1846 7.8655 0.0903 -0.4232 0.3217 0.3418 0.1454 0.5111 -0.5136 -0.6559 -0.2357 -0.0126 0.0176 0.0737 0.024 -0.0578 0.1142 15.8879 37.958 11.8618 9 4.9414 0.8065 -2.1649 0.6077 -0.711 3.0583 -0.0483 0.2488 0.2371 -0.0961 0.07 0.2147 -0.0243 -0.1181 -0.0217 0.0745 0.0157 -0.0281 0.0088 0.0147 0.0861 24.6469 35.7905 -1.9507 10 4.9204 -3.3742 2.4493 4.5127 -1.6342 3.0221 -0.0682 -0.0475 0.1023 -0.0301 0.0818 -0.0559 -0.0751 -0.0233 -0.0136 0.0449 -0.0165 -0.0112 0.0234 0.0101 0.0387 40.4735 35.6662 4.9837 11 9.327 0.8149 -0.4229 2.3177 -1.1896 4.2501 0.0512 -0.6908 -0.117 0.2733 -0.2179 -0.0975 -0.1143 0.1589 0.1666 0.0323 -0.0186 -0.0154 0.0491 0.024 0.0143 35.9517 28.7526 12.4712 12 1.5402 1.2578 -0.5272 1.0279 -0.4153 0.5174 -0.1273 0.2668 -0.0805 -0.0648 0.1223 0.0314 0.0451 -0.0789 0.005 0.0215 -0.007 0.0074 0.0294 -0.0137 0.0386 23.2385 22.764 1.0792 13 0.9995 0.4295 -0.4725 1.9384 -0.4447 1.7531 0.0877 0.0029 0.0188 -0.1311 0.0061 -0.147 -0.0254 0.0198 -0.0938 -0.0009 -0.0025 0.0085 0.0436 -0.0099 0.0515 18.7707 20.383 11.0035 14 19.2138 -14.5842 0.4881 12.5676 -3.8792 8.2332 -0.1248 -0.6829 -0.0983 0.8532 0.141 -0.9213 -0.0484 0.8757 -0.0162 0.007 0.0187 -0.0921 0.1104 -0.0024 0.0543 22.7732 15.9186 17.8089 15 1.9788 -0.1816 -0.0942 1.2862 -0.3518 1.5018 0.0485 -0.0236 -0.0395 0.0248 -0.0118 0.0467 0.0708 -0.0686 -0.0367 0.0521 0.0008 -0.0055 0.0355 -0.0052 0.04 3.6752 16.2585 14.5137 16 12.0046 -7.5717 8.2453 11.5696 -7.5385 6.4677 0.0141 -0.1005 -0.4137 -0.1784 0.331 0.3862 0.1896 -0.0214 -0.3451 0.0527 -0.0221 -0.0073 0.065 0.0221 -0.0002 0.5204 2.9993 20.843 17 1.2166 0.3997 -0.4557 1.3622 -1.0039 1.7544 0.0214 0.0053 -0.054 -0.0311 0.0463 0.052 0.096 -0.0926 -0.0678 0.0797 -0.0012 -0.0152 0.0454 -0.014 0.0399 3.0019 11.0204 12.9922 18 12.7497 4.6827 13.321 13.0001 9.8273 22.0604 0.1482 0.6364 -0.3206 -0.5301 -0.1998 -1.144 -0.1735 1.7418 0.0515 -0.0663 0.0824 0.0729 0.1218 0.0802 0.116 28.0252 10.1262 9.4733 19 6.423 0.4046 -1.1295 0.2256 -0.1874 1.6737 -0.1265 0.3615 0.0471 -0.0511 0.1009 -0.0786 0.1733 -0.0785 0.0256 0.0973 0.011 0.004 0.0312 -0.0172 0.0564 8.949 12.035 5.0976 20 1.2848 -0.8978 -1.123 2.9186 2.9842 6.5785 0.0596 -0.0474 -0.0712 0.0471 0.0347 -0.0086 0.1123 -0.0282 -0.0943 0.0542 -0.0053 0.0059 0.04 0.0022 0.0148 2.3408 12.6476 20.8883
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 - 11 1 - 11 2 X-RAY DIFFRACTION 2 AA12 - 18 12 - 18 3 X-RAY DIFFRACTION 3 AA19 - 33 19 - 33 4 X-RAY DIFFRACTION 4 AA34 - 39 34 - 39 5 X-RAY DIFFRACTION 5 AA40 - 60 40 - 60 6 X-RAY DIFFRACTION 6 AA61 - 75 61 - 75 7 X-RAY DIFFRACTION 7 AA76 - 83 76 - 83 8 X-RAY DIFFRACTION 8 AA84 - 95 84 - 95 9 X-RAY DIFFRACTION 9 AA96 - 106 96 - 106 10 X-RAY DIFFRACTION 10 AA107 - 124 107 - 124 11 X-RAY DIFFRACTION 11 BB1 - 11 1 - 11 12 X-RAY DIFFRACTION 12 BB12 - 26 12 - 26 13 X-RAY DIFFRACTION 13 BB27 - 33 27 - 33 14 X-RAY DIFFRACTION 14 BB34 - 39 34 - 39 15 X-RAY DIFFRACTION 15 BB40 - 61 40 - 61 16 X-RAY DIFFRACTION 16 BB62 - 68 62 - 68 17 X-RAY DIFFRACTION 17 BB69 - 86 69 - 86 18 X-RAY DIFFRACTION 18 BB87 - 95 87 - 95 19 X-RAY DIFFRACTION 19 BB96 - 106 96 - 106 20 X-RAY DIFFRACTION 20 BB107 - 124 107 - 124