Software Name Version Classification PHENIX1.9_1692refinement HKL-2000data collection HKL-2000data scaling AutoSolphasing PDB_EXTRACT3.25 data extraction PHENIXmodel building BUCCANEERmodel building HKL-2000data reduction
Refinement Method to determine structure : SAD / Resolution : 2.501→31.641 Å / SU ML : 0.44 / Cross valid method : THROUGHOUT / σ(F) : 1.34 / Phase error : 31.45 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2727 3958 2.19 % Rwork 0.2417 177057 - obs 0.2424 181015 99.21 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 329.3 Å2 / Biso mean : 82.1693 Å2 / Biso min : 32.32 Å2 Refinement step Cycle : final / Resolution : 2.501→31.641 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 13296 0 0 36 13332 Biso mean - - - 55.14 - Num. residues - - - - 1726
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.003 13534 X-RAY DIFFRACTION f_angle_d0.81 18340 X-RAY DIFFRACTION f_chiral_restr0.032 2093 X-RAY DIFFRACTION f_plane_restr0.004 2364 X-RAY DIFFRACTION f_dihedral_angle_d13.163 4762
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Rms Type 1 1 A7397 X-RAY DIFFRACTION 9.89 TORSIONAL1 2 B7397 X-RAY DIFFRACTION 9.89 TORSIONAL1 3 C7397 X-RAY DIFFRACTION 9.89 TORSIONAL1 4 D7397 X-RAY DIFFRACTION 9.89 TORSIONAL
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0
Show large table (6 x 28) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork % reflection obs (%)2.5012-2.5317 0.349 137 0.341 6049 94 2.5317-2.5638 0.3954 137 0.3369 6211 98 2.5638-2.5975 0.3835 142 0.3313 6270 98 2.5975-2.633 0.374 140 0.3347 6270 99 2.633-2.6706 0.3955 140 0.3337 6262 99 2.6706-2.7105 0.3559 139 0.3344 6305 99 2.7105-2.7528 0.3804 143 0.3227 6384 99 2.7528-2.7979 0.3719 138 0.3212 6263 99 2.7979-2.8461 0.3643 139 0.3158 6283 99 2.8461-2.8979 0.3179 140 0.2986 6285 99 2.8979-2.9536 0.3247 146 0.297 6378 99 2.9536-3.0138 0.3417 142 0.2971 6369 99 3.0138-3.0793 0.3665 138 0.293 6261 99 3.0793-3.1508 0.3202 146 0.2798 6382 99 3.1508-3.2296 0.3041 140 0.2806 6352 100 3.2296-3.3168 0.3286 140 0.2723 6343 100 3.3168-3.4143 0.3033 140 0.2489 6322 100 3.4143-3.5244 0.2802 143 0.2462 6385 100 3.5244-3.6501 0.2935 145 0.2323 6346 100 3.6501-3.7961 0.2416 140 0.2326 6337 100 3.7961-3.9685 0.2136 144 0.2233 6426 100 3.9685-4.1773 0.2738 141 0.2116 6344 100 4.1773-4.4384 0.2489 143 0.2068 6402 100 4.4384-4.78 0.1911 142 0.1918 6359 100 4.78-5.259 0.2336 144 0.2023 6358 100 5.259-6.0155 0.2754 143 0.2334 6398 100 6.0155-7.5618 0.3128 143 0.2463 6359 100 7.5618-31.641 0.1923 143 0.2067 6354 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 13) 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 1.4312 1.1242 1.5481 3.9572 1.2267 1.9229 -0.1674 0.4112 0.1353 -0.3272 0.0251 -0.0068 -0.0533 -0.1082 0.1881 0.4651 0.0138 0.1308 0.5711 0.0444 0.3902 -24.7185 23.4043 -9.747 2 2.9506 0.0357 -1.1978 1.4198 0.4102 3.2418 -0.3469 0.5389 -0.2785 -0.0189 0.0154 0.14 0.6905 -0.5114 0.2985 0.6453 -0.1405 0.1082 0.4967 -0.061 0.417 -33.7342 9.176 -6.5766 3 3.9019 0.2635 1.5147 5.8191 1.5842 6.7264 -0.3119 0.9457 -0.1022 -0.7686 -0.1021 0.3521 0.3807 -0.598 0.4148 0.6385 -0.1563 0.1797 0.8792 -0.0781 0.5212 -58.5357 12.0181 5.6255 4 4.2031 1.9759 2.026 6.7374 1.0067 3.6115 0.092 -0.5647 -0.7521 0.3516 -0.0894 -0.2408 0.8041 -0.1563 -0.033 0.6041 -0.0413 0.2095 0.5916 0.1494 0.5255 -17.3965 3.1948 17.638 5 5.5509 0.0081 1.1832 0.7117 0.005 0.0825 -0.0588 -0.4684 -0.0737 0.0485 0.0553 -0.082 -0.0447 0.1068 0.0503 0.5531 0.0107 0.1511 0.6308 0.0817 0.409 -6.579 12.304 20.4203 6 3.0281 -2.4509 -0.1295 1.969 0.1172 0.0774 0.0327 -1.0755 1.4176 1.0313 0.1191 0.4662 -0.5616 -0.3836 0.0701 0.7251 0.0089 0.1658 0.9481 -0.3721 0.9093 -49.2497 31.2022 31.9122 7 4.2868 0.3428 0.4196 3.0764 0.0653 4.3382 0.0397 -1.1105 0.2837 0.3701 -0.1336 -0.0706 0.3886 0.2763 0.1425 0.6477 -0.04 0.225 1.069 -0.1422 0.4953 -42.4409 20.2286 33.1403 8 2.1831 -0.5155 0.5599 2.8813 -0.6454 2.2099 -0.0954 -0.5049 0.1602 0.3473 0.1045 0.1564 -0.0832 -0.2135 -0.0403 0.4667 0.0362 0.1622 0.4883 -0.0232 0.4383 -22.3278 46.6075 9.1666 9 2.4047 -0.0584 0.8186 1.0295 0.5972 2.6881 -0.3305 -1.0581 0.1802 0.14 0.0896 0.2108 -0.5193 -0.9575 0.145 0.6931 0.2295 0.2067 0.7381 -0.1514 0.7607 -40.3645 60.0218 9.1455 10 6.2341 0.0978 -0.5445 3.4359 0.4128 6.5183 -0.1012 -0.4951 -0.7396 0.3452 -0.2548 0.6221 -0.1856 -0.9847 0.3819 0.6226 0.1656 0.1016 0.7452 -0.1341 0.8401 -57.5835 56.4872 -9.0575 11 5.5722 -0.8343 -0.8688 2.2906 0.3334 3.5623 0.0245 0.8038 1.1049 -0.5087 -0.0579 0.0912 -0.8349 0.0687 0.0797 0.5619 0.0131 0.0153 0.416 0.2328 0.6074 -15.5215 63.2245 -17.0253 12 6.1134 -0.4429 -0.5499 1.0888 0.6614 1.7341 -0.0474 1.0973 0.3007 -0.3669 -0.1278 -0.1235 -0.347 0.4733 0.0575 0.6592 0.0359 0.0871 0.66 0.1535 0.5238 -5.8696 54.0664 -23.4411 13 5.175 -0.1779 -2.5782 4.1544 1.0924 5.9963 -0.0448 1.5558 -0.9971 -0.6067 -0.3709 0.1961 -0.0035 -0.7017 0.3771 0.6913 0.1639 0.0327 1.0305 -0.3527 0.8231 -42.4863 48.1688 -35.1842
Refinement TLS group ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 2 through 164 )A2 - 164 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 165 through 340 )A165 - 340 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 341 through 476 )A341 - 476 4 X-RAY DIFFRACTION 4 chain 'B' and (resid 2 through 176 )B2 - 176 5 X-RAY DIFFRACTION 5 chain 'B' and (resid 177 through 288 )B177 - 288 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 289 through 315 )B289 - 315 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 316 through 476 )B316 - 476 8 X-RAY DIFFRACTION 8 chain 'C' and (resid 2 through 220 )C2 - 220 9 X-RAY DIFFRACTION 9 chain 'C' and (resid 221 through 315 )C221 - 315 10 X-RAY DIFFRACTION 10 chain 'C' and (resid 316 through 475 )C316 - 475 11 X-RAY DIFFRACTION 11 chain 'D' and (resid 2 through 202 )D2 - 202 12 X-RAY DIFFRACTION 12 chain 'D' and (resid 203 through 290 )D203 - 290 13 X-RAY DIFFRACTION 13 chain 'D' and (resid 291 through 475 )D