Software Name Version Classification PHENIX1.21_5207refinement XSCALE20210323 data scaling XDS20210323 data reduction PHASER2.8.3phasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 1.63→42.71 Å / SU ML : 0.16 / Cross valid method : THROUGHOUT / σ(F) : 1.37 / Phase error : 16.67 / Stereochemistry target values : MLDetails: TLS were used in refinement TLS DETAILS. NUMBER OF TLS GROUPS: 15 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain 'A' and (resid 2 through 20 ) ORIGIN FOR THE GROUP (A): -4.6308 16. ... Details : TLS were used in refinement TLS DETAILS. NUMBER OF TLS GROUPS: 15 ORIGIN: CENTER OF MASS TLS GROUP : 1 SELECTION: chain 'A' and (resid 2 through 20 ) ORIGIN FOR THE GROUP (A): -4.6308 16.5019 -9.7772 T TENSOR T11: 0.1927 T22: 0.1642 T33: 0.2009 T12: -0.0028 T13: -0.0230 T23: -0.0098 L TENSOR L11: 0.0558 L22: 0.1118 L33: 0.3906 L12: 0.0761 L13: 0.1538 L23: 0.2250 S TENSOR S11: 0.0676 S12: -0.0957 S13: -0.1023 S21: 0.0052 S22: -0.0523 S23: -0.0398 S31: 0.1943 S32: 0.0629 S33: 0.0001 TLS GROUP : 2 SELECTION: chain 'A' and (resid 21 through 84 ) ORIGIN FOR THE GROUP (A): -7.1860 16.9285 0.6502 T TENSOR T11: 0.2073 T22: 0.1618 T33: 0.1817 T12: -0.0039 T13: -0.0150 T23: 0.0314 L TENSOR L11: 0.3000 L22: 0.6249 L33: 0.6451 L12: 0.3691 L13: -0.0577 L23: 0.2460 S TENSOR S11: 0.0705 S12: -0.0710 S13: -0.0979 S21: 0.2006 S22: -0.0545 S23: -0.0257 S31: 0.2029 S32: -0.0568 S33: 0.0002 TLS GROUP : 3 SELECTION: chain 'A' and (resid 85 through 185 ) ORIGIN FOR THE GROUP (A): -9.8970 30.8504 -9.2245 T TENSOR T11: 0.1288 T22: 0.1286 T33: 0.1582 T12: 0.0064 T13: -0.0053 T23: -0.0041 L TENSOR L11: 0.5347 L22: 0.5469 L33: 0.4977 L12: 0.1294 L13: -0.0254 L23: 0.0947 S TENSOR S11: -0.0074 S12: -0.0272 S13: 0.0215 S21: 0.0219 S22: 0.0219 S23: 0.0611 S31: 0.0155 S32: -0.0197 S33: -0.0000 TLS GROUP : 4 SELECTION: chain 'A' and (resid 186 through 246 ) ORIGIN FOR THE GROUP (A): -3.9971 23.6931 -22.8305 T TENSOR T11: 0.1541 T22: 0.1469 T33: 0.1474 T12: -0.0046 T13: -0.0016 T23: -0.0111 L TENSOR L11: 0.4427 L22: 0.2773 L33: 0.1907 L12: -0.0903 L13: 0.0798 L23: 0.0186 S TENSOR S11: -0.0181 S12: 0.0763 S13: -0.0427 S21: -0.0485 S22: 0.0337 S23: -0.0124 S31: -0.0370 S32: 0.1025 S33: -0.0000 TLS GROUP : 5 SELECTION: chain 'A' and (resid 247 through 277 ) ORIGIN FOR THE GROUP (A): 1.3258 16.6523 -22.6549 T TENSOR T11: 0.1576 T22: 0.1645 T33: 0.1747 T12: 0.0269 T13: -0.0034 T23: -0.0317 L TENSOR L11: 0.1060 L22: 0.3129 L33: 0.3345 L12: -0.0810 L13: 0.1743 L23: 0.1541 S TENSOR S11: 0.0689 S12: 0.0255 S13: -0.0700 S21: 0.0461 S22: -0.0215 S23: -0.0349 S31: 0.0282 S32: 0.2609 S33: -0.0048 TLS GROUP : 6 SELECTION: chain 'A' and (resid 278 through 305 ) ORIGIN FOR THE GROUP (A): -1.6435 5.5827 -14.6457 T TENSOR T11: 0.2525 T22: 0.1632 T33: 0.2628 T12: 0.0408 T13: -0.0276 T23: -0.0134 L TENSOR L11: 0.0894 L22: 0.1110 L33: 0.5350 L12: -0.0173 L13: -0.0790 L23: 0.2398 S TENSOR S11: -0.1228 S12: -0.0741 S13: -0.4532 S21: 0.3292 S22: -0.0291 S23: -0.1298 S31: 0.6060 S32: 0.1017 S33: -0.0071 TLS GROUP : 7 SELECTION: chain 'B' and (resid 1 through 20 ) ORIGIN FOR THE GROUP (A): -39.0059 19.4217 -34.1021 T TENSOR T11: 0.1581 T22: 0.2108 T33: 0.1867 T12: 0.0040 T13: 0.0123 T23: 0.0033 L TENSOR L11: 0.1213 L22: 0.0800 L33: 0.4310 L12: 0.0097 L13: 0.2148 L23: -0.0853 S TENSOR S11: -0.0477 S12: -0.0284 S13: -0.0893 S21: 0.0283 S22: 0.0348 S23: 0.0230 S31: 0.2385 S32: -0.1119 S33: 0.0001 TLS GROUP : 8 SELECTION: chain 'B' and (resid 21 through 52 ) ORIGIN FOR THE GROUP (A): -38.2971 14.5567 -41.5819 T TENSOR T11: 0.2010 T22: 0.1815 T33: 0.1633 T12: -0.0385 T13: 0.0020 T23: -0.0153 L TENSOR L11: 0.1575 L22: 0.1244 L33: 0.4539 L12: 0.0216 L13: 0.1372 L23: -0.2981 S TENSOR S11: 0.0047 S12: 0.0640 S13: -0.1072 S21: -0.1262 S22: 0.0048 S23: 0.0246 S31: 0.2405 S32: -0.1639 S33: 0.0021 TLS GROUP : 9 SELECTION: chain 'B' and (resid 53 through 84 ) ORIGIN FOR THE GROUP (A): -32.2682 23.2516 -48.3338 T TENSOR T11: 0.1559 T22: 0.2003 T33: 0.1564 T12: -0.0159 T13: -0.0037 T23: -0.0140 L TENSOR L11: 0.0286 L22: 0.2819 L33: 0.4686 L12: -0.0237 L13: 0.0099 L23: 0.0556 S TENSOR S11: 0.0205 S12: 0.0669 S13: 0.0035 S21: -0.1042 S22: 0.0268 S23: -0.0124 S31: 0.0817 S32: 0.0170 S33: 0.0000 TLS GROUP : 10 SELECTION: chain 'B' and (resid 85 through 138 ) ORIGIN FOR THE GROUP (A): -29.3329 29.6624 -39.7053 T TENSOR T11: 0.1144 T22: 0.1594 T33: 0.1351 T12: -0.0046 T13: -0.0051 T23: 0.0061 L TENSOR L11: 0.0166 L22: 0.3761 L33: 0.5540 L12: 0.0602 L13: 0.0178 L23: 0.3342 S TENSOR S11: -0.0070 S12: 0.0420 S13: 0.0132 S21: -0.0208 S22: 0.0348 S23: -0.0105 S31: 0.0161 S32: -0.0149 S33: 0.0000 TLS GROUP : 11 SELECTION: chain 'B' and (resid 139 through 216 ) ORIGIN FOR THE GROUP (A): -32.0807 31.2161 -27.9941 T TENSOR T11: 0.1474 T22: 0.1457 T33: 0.1441 T12: 0.0040 T13: -0.0058 T23: 0.0033 L TENSOR L11: 0.1775 L22: 0.3135 L33: 0.6299 L12: 0.3057 L13: -0.1453 L23: 0.0916 S TENSOR S11: -0.0277 S12: -0.0295 S13: 0.0266 S21: 0.1021 S22: 0.0183 S23: -0.0435 S31: -0.0580 S32: -0.0669 S33: -0.0002 TLS GROUP : 12 SELECTION: chain 'B' and (resid 217 through 231 ) ORIGIN FOR THE GROUP (A): -37.0002 30.2209 -15.3864 T TENSOR T11: 0.2437 T22: 0.2093 T33: 0.1521 T12: -0.0160 T13: 0.0262 T23: 0.0097 L TENSOR L11: 0.0280 L22: 0.0301 L33: 0.0584 L12: 0.0314 L13: 0.0515 L23: 0.0143 S TENSOR S11: 0.0678 S12: -0.1291 S13: -0.0430 S21: 0.4576 S22: -0.0824 S23: 0.0546 S31: -0.0800 S32: -0.1094 S33: 0.0000 TLS GROUP : 13 SELECTION: chain 'B' and (resid 232 through 246 ) ORIGIN FOR THE GROUP (A): -38.4898 24.4467 -23.9162 T TENSOR T11: 0.2194 T22: 0.1712 T33: 0.1654 T12: -0.0126 T13: 0.0155 T23: -0.0070 L TENSOR L11: 0.0700 L22: 0.0398 L33: 0.1241 L12: 0.0597 L13: -0.0675 L23: -0.0260 S TENSOR S11: 0.0417 S12: -0.0871 S13: 0.0069 S21: 0.1881 S22: -0.1035 S23: 0.1380 S31: 0.0575 S32: -0.1808 S33: -0.0025 TLS GROUP : 14 SELECTION: chain 'B' and (resid 247 through 263 ) ORIGIN FOR THE GROUP (A): -43.8889 19.5534 -16.1059 T TENSOR T11: 0.2575 T22: 0.2404 T33: 0.1739 T12: -0.0431 T13: 0.0336 T23: -0.0024 L TENSOR L11: 0.0283 L22: 0.0270 L33: 0.0740 L12: -0.0218 L13: -0.0114 L23: -0.0163 S TENSOR S11: -0.0132 S12: -0.0626 S13: -0.0430 S21: 0.2340 S22: -0.0338 S23: 0.0866 S31: 0.1874 S32: -0.3468 S33: -0.0001 TLS GROUP : 15 SELECTION: chain 'B' and (resid 264 through 305 ) ORIGIN FOR THE GROUP (A): -42.0222 13.2385 -28.5887 T TENSOR T11: 0.2185 T22: 0.1841 T33: 0.1706 T12: -0.0530 T13: -0.0042 T23: 0.0118 L TENSOR L11: 0.1772 L22: 0.1531 L33: 0.5268 L12: 0.0156 L13: 0.1172 L23: -0.2397 S TENSOR S11: 0.0627 S12: 0.0128 S13: -0.0739 S21: -0.1086 S22: -0.0308 S23: 0.0591 S31: 0.2241 S32: -0.2015 S33: 0.0000Rfactor Num. reflection % reflection Rfree 0.1744 3665 5 % Rwork 0.1428 - - obs 0.1444 73338 99.65 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 19.18 Å2 Refinement step Cycle : LAST / Resolution : 1.63→42.71 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 4749 0 146 944 5839
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.008 5245 X-RAY DIFFRACTION f_angle_d0.919 7215 X-RAY DIFFRACTION f_dihedral_angle_d13.856 2068 X-RAY DIFFRACTION f_chiral_restr0.06 810 X-RAY DIFFRACTION f_plane_restr0.008 917
LS refinement shell Show large table (7 x 26) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.63-1.65 0.2604 129 0.2068 2456 X-RAY DIFFRACTION 92 1.65-1.67 0.2387 139 0.1779 2645 X-RAY DIFFRACTION 100 1.67-1.7 0.221 138 0.1678 2650 X-RAY DIFFRACTION 100 1.7-1.72 0.1783 140 0.1622 2655 X-RAY DIFFRACTION 100 1.72-1.75 0.2164 141 0.1668 2668 X-RAY DIFFRACTION 100 1.75-1.78 0.216 137 0.1707 2622 X-RAY DIFFRACTION 100 1.78-1.81 0.2431 140 0.1902 2670 X-RAY DIFFRACTION 100 1.81-1.84 0.2995 140 0.2091 2661 X-RAY DIFFRACTION 100 1.84-1.88 0.2408 140 0.1896 2653 X-RAY DIFFRACTION 100 1.88-1.92 0.2004 141 0.1723 2667 X-RAY DIFFRACTION 100 1.92-1.96 0.1839 141 0.1577 2679 X-RAY DIFFRACTION 100 1.96-2 0.2163 139 0.1451 2655 X-RAY DIFFRACTION 100 2-2.05 0.1777 141 0.1428 2673 X-RAY DIFFRACTION 100 2.05-2.11 0.183 140 0.14 2664 X-RAY DIFFRACTION 100 2.11-2.17 0.1727 142 0.146 2685 X-RAY DIFFRACTION 100 2.17-2.24 0.1883 141 0.1463 2684 X-RAY DIFFRACTION 100 2.24-2.32 0.1936 141 0.1457 2674 X-RAY DIFFRACTION 100 2.32-2.41 0.1817 141 0.1414 2686 X-RAY DIFFRACTION 100 2.41-2.52 0.1677 142 0.1437 2691 X-RAY DIFFRACTION 100 2.52-2.66 0.1591 142 0.1374 2700 X-RAY DIFFRACTION 100 2.66-2.82 0.1912 142 0.1392 2696 X-RAY DIFFRACTION 100 2.82-3.04 0.1755 142 0.1423 2703 X-RAY DIFFRACTION 100 3.04-3.35 0.1586 144 0.1391 2741 X-RAY DIFFRACTION 100 3.35-3.83 0.1547 144 0.1275 2739 X-RAY DIFFRACTION 100 3.83-4.82 0.1315 146 0.11 2768 X-RAY DIFFRACTION 100 4.83-42.71 0.1403 152 0.1389 2888 X-RAY DIFFRACTION 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 15) 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 0.0558 0.0761 0.1538 0.1118 0.225 0.3906 0.0676 -0.0957 -0.1023 0.0052 -0.0523 -0.0398 0.1943 0.0629 0.0001 0.1927 -0.0028 -0.023 0.1642 -0.0098 0.2009 -4.6308 16.5019 -9.7772 2 0.3 0.3691 -0.0577 0.6249 0.246 0.6451 0.0705 -0.071 -0.0979 0.2006 -0.0545 -0.0257 0.2029 -0.0568 0.0002 0.2073 -0.0039 -0.015 0.1618 0.0314 0.1817 -7.186 16.9285 0.6502 3 0.5347 0.1294 -0.0254 0.5469 0.0947 0.4977 -0.0074 -0.0272 0.0215 0.0219 0.0219 0.0611 0.0155 -0.0197 -0 0.1288 0.0064 -0.0053 0.1286 -0.0041 0.1582 -9.897 30.8504 -9.2245 4 0.4427 -0.0903 0.0798 0.2773 0.0186 0.1907 -0.0181 0.0763 -0.0427 -0.0485 0.0337 -0.0124 -0.037 0.1025 -0 0.1541 -0.0046 -0.0016 0.1469 -0.0111 0.1474 -3.9971 23.6931 -22.8305 5 0.106 -0.081 0.1743 0.3129 0.1541 0.3345 0.0689 0.0255 -0.07 0.0461 -0.0215 -0.0349 0.0282 0.2609 -0.0048 0.1576 0.0269 -0.0034 0.1645 -0.0317 0.1747 1.3258 16.6523 -22.6549 6 0.0894 -0.0173 -0.079 0.111 0.2398 0.535 -0.1228 -0.0741 -0.4532 0.3292 -0.0291 -0.1298 0.606 0.1017 -0.0071 0.2525 0.0408 -0.0276 0.1632 -0.0134 0.2628 -1.6435 5.5827 -14.6457 7 0.1213 0.0097 0.2148 0.08 -0.0853 0.431 -0.0477 -0.0284 -0.0893 0.0283 0.0348 0.023 0.2385 -0.1119 0.0001 0.1581 0.004 0.0123 0.2108 0.0033 0.1867 -39.0059 19.4217 -34.1021 8 0.1575 0.0216 0.1372 0.1244 -0.2981 0.4539 0.0047 0.064 -0.1072 -0.1262 0.0048 0.0246 0.2405 -0.1639 0.0021 0.201 -0.0385 0.002 0.1815 -0.0153 0.1633 -38.2971 14.5567 -41.5819 9 0.0286 -0.0237 0.0099 0.2819 0.0556 0.4686 0.0205 0.0669 0.0035 -0.1042 0.0268 -0.0124 0.0817 0.017 0 0.1559 -0.0159 -0.0037 0.2003 -0.014 0.1564 -32.2682 23.2516 -48.3338 10 0.0166 0.0602 0.0178 0.3761 0.3342 0.554 -0.007 0.042 0.0132 -0.0208 0.0348 -0.0105 0.0161 -0.0149 0 0.1144 -0.0046 -0.0051 0.1594 0.0061 0.1351 -29.3329 29.6624 -39.7053 11 0.1775 0.3057 -0.1453 0.3135 0.0916 0.6299 -0.0277 -0.0295 0.0266 0.1021 0.0183 -0.0435 -0.058 -0.0669 -0.0002 0.1474 0.004 -0.0058 0.1457 0.0033 0.1441 -32.0807 31.2161 -27.9941 12 0.028 0.0314 0.0515 0.0301 0.0143 0.0584 0.0678 -0.1291 -0.043 0.4576 -0.0824 0.0546 -0.08 -0.1094 0 0.2437 -0.016 0.0262 0.2093 0.0097 0.1521 -37.0002 30.2209 -15.3864 13 0.07 0.0597 -0.0675 0.0398 -0.026 0.1241 0.0417 -0.0871 0.0069 0.1881 -0.1035 0.138 0.0575 -0.1808 -0.0025 0.2194 -0.0126 0.0155 0.1712 -0.007 0.1654 -38.4898 24.4467 -23.9162 14 0.0283 -0.0218 -0.0114 0.027 -0.0163 0.074 -0.0132 -0.0626 -0.043 0.234 -0.0338 0.0866 0.1874 -0.3468 -0.0001 0.2575 -0.0431 0.0336 0.2404 -0.0024 0.1739 -43.8889 19.5534 -16.1059 15 0.1772 0.0156 0.1172 0.1531 -0.2397 0.5268 0.0627 0.0128 -0.0739 -0.1086 -0.0308 0.0591 0.2241 -0.2015 0 0.2185 -0.053 -0.0042 0.1841 0.0118 0.1706 -42.0222 13.2385 -28.5887
Refinement TLS group ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 2 through 20 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 21 through 84 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 85 through 185 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 186 through 246 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 247 through 277 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 278 through 305 )7 X-RAY DIFFRACTION 7 chain 'B' and (resid 1 through 20 )8 X-RAY DIFFRACTION 8 chain 'B' and (resid 21 through 52 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 53 through 84 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 85 through 138 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 139 through 216 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 217 through 231 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 232 through 246 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 247 through 263 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 264 through 305 )