Software Name Version Classification NB DENZOdata reductionShow SCALEPACKdata scalingShow REFMAC5.5.0054refinementShow PDB_EXTRACT3.006 data extractionShow SBC-Collectdata collection HKL-3000data reduction HKL-3000data scaling SHELXDphasing MLPHAREphasing DMphasing SOLVEphasing RESOLVEphasing HKL-3000phasing
Refinement Method to determine structure : SAD / Resolution : 1.83→49.8 Å / Cor.coef. Fo :Fc : 0.966 / Cor.coef. Fo :Fc free : 0.952 / Occupancy max : 1 / Occupancy min : 0.4 / SU B : 4.661 / SU ML : 0.065 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / σ(I) : 0 / ESU R : 0.116 / ESU R Free : 0.108 / Stereochemistry target values : MAXIMUM LIKELIHOODDetails : 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLYRfactor Num. reflection % reflection Selection details Rfree 0.182 3951 5 % RANDOM Rwork 0.149 - - - all 0.151 78700 - - obs 0.151 78700 99.64 % -
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 : 50.91 Å2 / Biso mean : 17.208 Å2 / Biso min : 4.5 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.13 Å2 0 Å2 0 Å2 2- - -0.19 Å2 0 Å2 3- - - 0.06 Å2
Refinement step Cycle : LAST / Resolution : 1.83→49.8 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6648 0 4 716 7368
Refine LS restraints Show large table (5 x 16) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.019 0.022 7087 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 4726 X-RAY DIFFRACTION r_angle_refined_deg1.601 1.961 9681 X-RAY DIFFRACTION r_angle_other_deg0.991 3 11556 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.963 5 949 X-RAY DIFFRACTION r_dihedral_angle_2_deg35.152 22.318 289 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.453 15 1200 X-RAY DIFFRACTION r_dihedral_angle_4_deg22.422 15 61 X-RAY DIFFRACTION r_chiral_restr0.104 0.2 1158 X-RAY DIFFRACTION r_gen_planes_refined0.008 0.02 7955 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 1478 X-RAY DIFFRACTION r_mcbond_it1.002 1.5 4486 X-RAY DIFFRACTION r_mcbond_other0.322 1.5 1825 X-RAY DIFFRACTION r_mcangle_it1.76 2 7257 X-RAY DIFFRACTION r_scbond_it2.652 3 2601 X-RAY DIFFRACTION r_scangle_it4.275 4.5 2389
LS refinement shell Resolution : 1.83→1.88 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.272 253 - Rwork 0.216 5281 - all - 5534 - obs - 5534 95.71 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 32) 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 1.0451 -0.6679 -0.0369 1.9253 0.3194 1.2261 0.0211 0.1013 -0.1578 0.1456 0.0082 0.1032 0.1928 0.0001 -0.0293 0.0771 0.0365 -0.0138 0.0358 -0.0158 0.0397 29.8229 22.2258 21.3717 2 1.3376 0.4378 1.1663 1.3848 1.0333 2.9307 0.0862 0.002 -0.1967 0.1028 -0.0538 -0.0956 0.1818 -0.0307 -0.0324 0.0688 0.0456 -0.0247 0.047 -0.0123 0.0518 36.4898 20.1611 25.1448 3 1.1628 -0.7635 0.3508 1.319 0.1346 1.4848 -0.0722 0.0583 0.0813 0.0849 0.014 -0.206 0.0425 0.1611 0.0582 0.0305 0.0239 -0.0211 0.0503 0.0011 0.0559 39.1964 33.4604 24.656 4 0.9495 -0.3487 -0.319 0.8982 0.2037 1.487 -0.089 -0.0455 0.0023 0.1447 0.0269 -0.0759 0.0708 0.1105 0.0622 0.0451 0.0152 -0.0192 0.0339 0.0036 0.0226 30.8105 38.583 30.666 5 0.8346 -0.5902 -0.4224 1.0108 0.5414 1.1837 -0.0074 0.0087 -0.0728 0.0968 -0.0575 0.1215 0.0657 -0.0914 0.0648 0.0446 -0.0054 -0.0085 0.0437 -0.0048 0.032 18.9253 37.2292 27.6368 6 0.9123 -0.3845 0.1458 0.9187 0.6263 0.7069 -0.0012 0.0947 0.0258 -0.0615 -0.0264 -0.0232 -0.024 0.0307 0.0276 0.0464 0.0061 0.0057 0.0502 0.0124 0.0309 26.3419 39.9926 16.8216 7 9.2096 -7.6998 8.0323 6.4737 -6.7448 7.0297 -0.0377 -1.6254 -1.0509 -0.0768 1.0801 0.8297 0.0801 -1.3134 -1.0423 0.1379 -0.1418 0.0711 0.7429 0.2683 0.401 10.5899 22.4835 25.5083 8 1.9733 -0.5269 0.1328 0.7473 0.1713 0.8625 0.0345 0.0966 -0.1659 -0.0039 -0.0726 0.1304 0.059 -0.1136 0.0381 0.0494 0.0025 -0.0177 0.058 -0.019 0.0451 17.6598 29.7614 15.5753 9 0.8328 -0.6357 0.0809 1.8401 0.1624 0.915 -0.1126 -0.0515 0.2373 -0.0029 0.0342 -0.0791 -0.1739 -0.0939 0.0785 0.0866 0.0162 -0.0639 0.0245 -0.0296 0.1013 15.6919 67.6547 38.3575 10 3.5097 -0.6836 1.2764 0.4151 -0.6267 1.1963 -0.2558 -0.015 0.3771 0.0772 0.0275 -0.0701 -0.2072 0.0065 0.2282 0.1009 0.0042 -0.0939 0.036 -0.0257 0.1359 22.175 69.387 43.2146 11 2.6934 -0.5281 -0.3844 1.075 0.8616 1.8193 0.0056 -0.1986 -0.0257 0.2197 0.03 -0.087 0.0012 -0.0141 -0.0357 0.0944 0.0069 -0.0412 0.0432 -0.0177 0.0328 23.6329 55.7063 48.633 12 1.0743 -0.2652 0.0822 0.7399 0.4236 0.5832 -0.0205 0.0078 0.1133 0.0091 0.0415 -0.1583 -0.0649 0.0924 -0.0211 0.04 -0.0137 -0.0239 0.0291 -0.0061 0.0601 28.0383 53.1823 33.5456 13 1.2222 -0.4517 -0.2307 0.8258 -0.0823 1.4461 -0.0001 -0.0627 0.0653 0.0662 -0.0276 0.101 -0.1218 -0.0861 0.0278 0.0471 -0.0063 -0.0062 0.0337 -0.025 0.0434 12.9539 53.608 37.8576 14 0.7913 -0.1337 -0.0068 0.7331 0.1922 0.7081 -0.0034 0.0621 0.0154 0.0228 -0.0298 -0.0159 -0.0447 -0.0355 0.0332 0.0379 -0.0031 -0.0158 0.0269 -0.0006 0.026 17.4688 49.2807 30.5885 15 1.3575 -1.0073 1.4455 2.9768 0.1737 2.2363 -0.0968 0.3018 0.2709 -0.4272 -0.1059 -0.3391 -0.3734 0.3932 0.2027 0.1438 -0.0455 -0.0276 0.1017 0.0327 0.1307 14.5861 64.5694 22.8647 16 0.554 -0.0339 0.5821 1.0555 -0.3192 0.9687 -0.0515 0.0769 0.0593 -0.0396 -0.0869 0.0386 -0.0519 0.0071 0.1384 0.0445 0.0037 -0.0372 0.0583 -0.0195 0.0635 7.5089 57.9876 25.9943 17 1.4084 -0.1826 0.6281 1.1521 -0.3082 2.1069 -0.0521 -0.1404 0.0704 0.1438 0.0695 0.1201 -0.1271 -0.2994 -0.0174 0.0348 0.0437 0.0034 0.0888 -0.0032 0.0701 -16.8332 64.6856 20.4089 18 1.3747 -1.2377 0.3366 1.803 -0.4262 0.2642 0.0996 0.2531 -0.0248 -0.0448 -0.078 0.1813 -0.1018 -0.0689 -0.0216 0.1032 0.0993 -0.0122 0.1501 0.032 0.0619 -15.6287 61.9535 4.6406 19 0.5195 -0.311 0.0549 1.4739 0.1629 0.5982 -0.0231 0.0663 -0.0449 -0.0165 -0.0114 0.1738 -0.0126 -0.1156 0.0346 0.0077 -0.0003 -0.0149 0.061 -0.0013 0.055 -10.4244 51.5508 9.2795 20 0.7514 -0.373 0.1868 4.8143 -1.1574 1.3095 -0.0606 0.0061 0.108 0.2205 0.08 -0.1279 -0.1401 -0.0662 -0.0193 0.0283 0.0119 -0.0221 0.032 -0.0021 0.0472 -1.9444 60.7602 15.7479 21 1.1352 0.2688 0.2657 1.3756 0.3737 1.2591 -0.0074 -0.079 -0.1437 0.1769 0.0124 0.0936 0.1087 -0.0858 -0.005 0.0484 -0.0065 0.0003 0.0516 0.0054 0.0528 -4.1845 41.9707 17.8856 22 0.5538 -0.3418 -0.0591 1.1357 -0.1176 1.1637 -0.0121 0.0295 0.0979 -0.0173 -0.0037 -0.111 -0.0912 -0.0128 0.0157 0.0209 -0.0055 -0.0189 0.0312 0.0122 0.0491 2.7761 59.1297 11.3054 23 0.5881 1.0313 -0.1722 1.9426 -0.3736 0.0891 0.034 -0.0672 -0.0526 0.054 0.0422 0.071 0.0039 -0.0745 -0.0762 0.1261 -0.0541 -0.0171 0.264 0.1707 0.2388 -8.2139 44.8644 33.3604 24 1.2394 -0.2355 0.3203 0.4345 0.0079 0.938 -0.0372 -0.0819 0.0168 0.1151 0.0694 -0.0265 0.0006 -0.1314 -0.0322 0.0503 0.0128 -0.0256 0.0544 -0.01 0.0392 0.7655 57.6407 25.8997 25 2.1004 -0.2977 -0.4686 2.0022 0.9029 1.3666 -0.0425 0.2728 -0.1233 -0.2535 0.0297 -0.0822 0.0086 0.0823 0.0128 0.1022 -0.0187 0.003 0.0998 -0.0461 0.0484 8.3229 26.1523 -4.1398 26 5.9838 -2.6336 1.8919 4.2529 -0.9857 1.9757 -0.1931 0.5655 -0.0027 -0.1599 -0.0446 -0.1036 -0.0296 0.0281 0.2377 0.1146 -0.0389 -0.0222 0.1228 -0.0562 0.0726 4.1642 24.7629 -8.155 27 1.1576 -0.8329 0.1862 2.8978 2.1872 2.4449 0.1141 0.21 -0.2147 -0.3839 -0.2948 0.359 -0.1799 -0.1913 0.1808 0.2084 -0.0752 -0.048 0.1527 -0.0814 0.0971 -5.0673 26.9521 -6.5712 28 0.4702 -0.2095 -0.584 3.7825 0.1243 0.733 -0.0773 0.0942 -0.0937 -0.2055 -0.023 0.2239 0.101 -0.1069 0.1002 0.0612 -0.0397 -0.0155 0.0692 -0.0401 0.0751 0.3727 25.5393 1.5537 29 0.6549 -0.2835 -0.2543 3.0876 -0.7701 1.1094 0.0135 0.1672 -0.0838 -0.2136 -0.0386 0.119 0.0275 -0.1782 0.0251 0.0483 -0.012 -0.0282 0.0776 -0.0256 0.0416 -4.4388 38.6993 1.4744 30 0.5135 -0.4544 0.0071 1.6828 0.0413 0.7006 -0.043 0.0477 -0.0026 0.0135 0.029 -0.0873 0.029 -0.0635 0.014 0.0256 -0.0184 -0.0152 0.032 -0.0104 0.0356 3.5825 38.0266 9.3248 31 0.7929 0.7379 -0.5246 1.6937 -2.5377 4.6889 -0.0889 0.1475 -0.0544 -0.0838 0.0019 -0.156 0.0307 0.0876 0.087 0.0599 -0.0149 0.061 0.0934 0.0286 0.1642 12.4457 40.3978 -1.7138 32 0.7691 -0.665 0.4005 0.982 0.2087 1.1736 -0.0544 0.0639 0.0891 0.0191 0.0352 -0.1594 0.0117 0.1186 0.0191 0.0634 -0.0298 0.0059 0.0535 -0.0172 0.0854 15.3327 32.4585 7.8695
Refinement TLS group Show large table (5 x 32) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A5 - 26 2 X-RAY DIFFRACTION 2 A27 - 55 3 X-RAY DIFFRACTION 3 A56 - 86 4 X-RAY DIFFRACTION 4 A87 - 126 5 X-RAY DIFFRACTION 5 A127 - 155 6 X-RAY DIFFRACTION 6 A156 - 180 7 X-RAY DIFFRACTION 7 A181 - 205 8 X-RAY DIFFRACTION 8 A206 - 236 9 X-RAY DIFFRACTION 9 B3 - 26 10 X-RAY DIFFRACTION 10 B27 - 57 11 X-RAY DIFFRACTION 11 B58 - 78 12 X-RAY DIFFRACTION 12 B79 - 115 13 X-RAY DIFFRACTION 13 B116 - 139 14 X-RAY DIFFRACTION 14 B140 - 171 15 X-RAY DIFFRACTION 15 B172 - 213 16 X-RAY DIFFRACTION 16 B214 - 236 17 X-RAY DIFFRACTION 17 C5 - 54 18 X-RAY DIFFRACTION 18 C55 - 77 19 X-RAY DIFFRACTION 19 C78 - 122 20 X-RAY DIFFRACTION 20 C123 - 137 21 X-RAY DIFFRACTION 21 C138 - 156 22 X-RAY DIFFRACTION 22 C157 - 178 23 X-RAY DIFFRACTION 23 C179 - 206 24 X-RAY DIFFRACTION 24 C207 - 236 25 X-RAY DIFFRACTION 25 D5 - 26 26 X-RAY DIFFRACTION 26 D27 - 43 27 X-RAY DIFFRACTION 27 D44 - 73 28 X-RAY DIFFRACTION 28 D74 - 87 29 X-RAY DIFFRACTION 29 D88 - 126 30 X-RAY DIFFRACTION 30 D127 - 173 31 X-RAY DIFFRACTION 31 D174 - 203 32 X-RAY DIFFRACTION 32 D204 - 236