Software Name Version Classification HKL-2000data collection SHELXSphasing PHENIX(phenix.refine: 1.7.3_928)refinement HKL-2000data reduction HKL-2000data scaling
Refinement Method to determine structure : SAD / Resolution : 3.187→38.119 Å / SU ML : 0.33 / σ(F) : 1.96 / Phase error : 21.14 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2162 1994 4.39 % Rwork 0.1683 - - obs 0.1705 45435 99.52 %
Solvent computation Shrinkage radii : 0.86 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 19.409 Å2 / ksol : 0.309 e/Å3 Displacement parameters Baniso -1 Baniso -2 Baniso -3 1- -2.0524 Å2 -0 Å2 -0 Å2 2- - -2.0524 Å2 0 Å2 3- - - -2.7428 Å2
Refinement step Cycle : LAST / Resolution : 3.187→38.119 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 14034 358 0 34 14426
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.01 14742 X-RAY DIFFRACTION f_angle_d1.347 20024 X-RAY DIFFRACTION f_dihedral_angle_d17.055 5541 X-RAY DIFFRACTION f_chiral_restr0.089 2241 X-RAY DIFFRACTION f_plane_restr0.006 2500
Refine LS restraints NCS Show large table (7 x 16) Hide large table Ens-ID Dom-ID Auth asym-ID Number Refine-ID Type Rms dev position (Å)1 1 A505 X-RAY DIFFRACTION POSITIONAL1 2 B505 X-RAY DIFFRACTION POSITIONAL0.08 2 1 A419 X-RAY DIFFRACTION POSITIONAL2 2 B419 X-RAY DIFFRACTION POSITIONAL0.079 3 1 A1236 X-RAY DIFFRACTION POSITIONAL3 2 B1236 X-RAY DIFFRACTION POSITIONAL0.058 4 1 A402 X-RAY DIFFRACTION POSITIONAL4 2 B402 X-RAY DIFFRACTION POSITIONAL0.045 5 1 A909 X-RAY DIFFRACTION POSITIONAL5 2 B909 X-RAY DIFFRACTION POSITIONAL0.042 6 1 A2797 X-RAY DIFFRACTION POSITIONAL6 2 B2797 X-RAY DIFFRACTION POSITIONAL0.05 7 1 A178 X-RAY DIFFRACTION POSITIONAL7 2 B178 X-RAY DIFFRACTION POSITIONAL0.038 8 1 E179 X-RAY DIFFRACTION POSITIONAL8 2 F179 X-RAY DIFFRACTION POSITIONAL0.035
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)3.187-3.3012 0.3237 202 0.2332 4196 X-RAY DIFFRACTION 97 3.3012-3.4333 0.2598 206 0.2018 4357 X-RAY DIFFRACTION 100 3.4333-3.5894 0.2418 203 0.1844 4351 X-RAY DIFFRACTION 100 3.5894-3.7785 0.248 206 0.1782 4391 X-RAY DIFFRACTION 100 3.7785-4.015 0.2313 185 0.163 4359 X-RAY DIFFRACTION 100 4.015-4.3246 0.1939 210 0.1294 4378 X-RAY DIFFRACTION 100 4.3246-4.7591 0.1381 187 0.115 4371 X-RAY DIFFRACTION 100 4.7591-5.446 0.1965 199 0.1422 4371 X-RAY DIFFRACTION 100 5.446-6.8549 0.2195 193 0.1865 4365 X-RAY DIFFRACTION 100 6.8549-38.1219 0.1997 203 0.2017 4302 X-RAY DIFFRACTION 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 12) 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 0.7474 0.0869 -0.3122 1.022 -0.2878 0.8915 -0.0158 0.1545 -0.1436 -0.1019 -0.0301 -0.0944 0.2449 -0.0004 -0.0243 0.0648 0.0036 -0.0527 0.0822 -0.0629 0.0738 99.6553 21.4454 -20.2741 2 5.9203 -0.6256 0.3824 5.0301 -1.7887 1.1572 -0.1173 0.8305 0.1546 -0.222 -0.1453 -1.5157 0.1382 0.4411 0.0028 0.4464 0.1006 0.1423 0.3294 -0.0213 0.6883 117.2963 7.5789 -31.6441 3 2.1759 0.0303 -0.7636 0.9161 0.316 1.4554 0.2537 0.1576 0.2822 -0.4595 -0.1116 -0.6327 -0.1631 0.4892 -0.196 0.3337 0.1501 0.2329 0.4153 0.1156 0.4526 125.7622 39.5101 -43.6302 4 0.5504 0.0848 0.2205 0.5679 0.0579 0.7156 0.1189 -0.0074 -0.0966 0.1223 0.0615 -0.1969 0.0661 0.0734 -0.0145 0.0468 -0.0126 -0.0125 0.0155 0.0296 -0.0584 103.5866 34.1606 3.1871 5 1.2459 0.2871 -0.125 1.0554 -0.0385 1.0919 0.0135 0.0252 0.2277 -0.0566 0.0398 -0.2975 -0.2113 0.2759 0.0051 0.0632 -0.1364 -0.0453 0.1059 -0.0096 0.2416 121.2074 57.7277 0.6156 6 1.1996 -0.3196 -0.467 0.9503 -0.1659 1.5165 -0.1666 -0.1436 -0.1991 0.2211 0.0071 -0.1698 0.2273 0.2497 0.0142 0.1299 0.0237 -0.0383 0.0502 0.0185 0.128 190.1728 74.8197 22.6148 7 2.8976 -1.1365 -0.9878 2.3595 0.9519 2.4343 -0.2384 -0.1854 -0.7729 0.1898 -0.147 0.7323 0.2162 -0.3371 0.2305 0.2739 0.1506 0.2027 0.2543 0.0759 0.4545 195.4183 52.9732 33.6162 8 1.0113 0.2406 -0.2824 3.3092 -0.985 1.3759 -0.2101 -0.1099 -0.177 0.2539 0.3588 0.62 0.1406 -0.2926 -0.2402 0.5096 0.0741 0.2164 0.1841 0.1339 0.3115 162.6851 63.0293 41.7592 9 0.8763 -0.2433 0.2957 0.8763 -0.0837 0.7116 0.2027 0.247 -0.2825 -0.2693 -0.0637 -0.0253 0.2477 0.0515 -0.0189 0.1796 0.0939 -0.0043 0.0197 0.0147 0.0076 178.0417 76.2857 -1.7914 10 1.3567 0.0568 0.1258 0.7911 0.1108 0.8419 0.0182 -0.1089 -0.2177 -0.0589 -0.0014 0.2464 0.1742 -0.3571 -0.005 0.0971 -0.1261 -0.1636 0.241 0.0399 0.146 149.049 70.7535 -0.1257 11 0.052 0.0076 0.0148 0.0053 -0.0017 0.0172 0.0015 0.0133 -0.0198 -0.0004 0.0047 -0.0081 0.0037 0.006 -0.0239 0.0239 0.0045 -0.0223 0.0171 -0.0258 0.0423 107.9276 44.3556 -10.4682 12 0.0232 -0.0161 0.0242 0.0253 -0.0034 0.0388 0.0017 -0.0037 -0.012 -0.0339 -0.0021 0.0531 0.0049 -0.0277 -0.0853 0.0253 0.0448 -0.0533 0.0631 0.015 0.0841 166.5308 76.7295 11.6021
Refinement TLS group Show large table (6 x 18) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 ( CHAIN A AND ( RESID 217:274 OR RESID 396:494 OR RESID 671:712 ) )A217 - 274 2 X-RAY DIFFRACTION 1 ( CHAIN A AND ( RESID 217:274 OR RESID 396:494 OR RESID 671:712 ) )A396 - 494 3 X-RAY DIFFRACTION 1 ( CHAIN A AND ( RESID 217:274 OR RESID 396:494 OR RESID 671:712 ) )A671 - 712 4 X-RAY DIFFRACTION 2 ( CHAIN A AND RESID 275:395 )A275 - 395 5 X-RAY DIFFRACTION 3 ( CHAIN A AND RESID 495:670 )A495 - 670 6 X-RAY DIFFRACTION 4 ( CHAIN A AND ( RESID 722:773 OR RESID 947:1251 ) )A722 - 773 7 X-RAY DIFFRACTION 4 ( CHAIN A AND ( RESID 722:773 OR RESID 947:1251 ) )A947 - 1251 8 X-RAY DIFFRACTION 5 ( CHAIN A AND RESID 774:946 )A774 - 946 9 X-RAY DIFFRACTION 6 ( CHAIN B AND ( RESID 220:274 OR RESID 396:494 OR RESID 671:710 ) )B220 - 274 10 X-RAY DIFFRACTION 6 ( CHAIN B AND ( RESID 220:274