Software | Name | Version | Classification |
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PHENIX | (phenix.refine: 1.8.2_1309)refinementPDB_EXTRACT | 3.15 | data extraction | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→32.384 Å / FOM work R set: 0.847 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.95 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2314 | 1912 | 6.85 % |
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Rwork | 0.1962 | 25981 | - |
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obs | 0.1986 | 27893 | 93.64 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso max: 105.77 Å2 / Biso mean: 37.96 Å2 / Biso min: 9.31 Å2 |
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Refinement step | Cycle: final / Resolution: 2.05→32.384 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2989 | 0 | 0 | 269 | 3258 |
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Biso mean | - | - | - | 38.62 | - |
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Num. residues | - | - | - | - | 359 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.005 | 3034 | X-RAY DIFFRACTION | f_angle_d0.942 | 4084 | X-RAY DIFFRACTION | f_chiral_restr0.067 | 452 | X-RAY DIFFRACTION | f_plane_restr0.004 | 532 | X-RAY DIFFRACTION | f_dihedral_angle_d13.832 | 1191 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Number | Refine-ID | Rms | Type |
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1 | 1 | A1770 | X-RAY DIFFRACTION | 11.352 | TORSIONAL1 | 2 | B1770 | X-RAY DIFFRACTION | 11.352 | TORSIONAL1 | 3 | C1770 | X-RAY DIFFRACTION | 11.352 | TORSIONAL | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.05-2.1013 | 0.3002 | 124 | 0.2832 | 1645 | 1769 | 85 | 2.1013-2.1581 | 0.2467 | 126 | 0.2577 | 1740 | 1866 | 87 | 2.1581-2.2216 | 0.2642 | 125 | 0.2435 | 1741 | 1866 | 89 | 2.2216-2.2932 | 0.2721 | 135 | 0.2313 | 1771 | 1906 | 90 | 2.2932-2.3752 | 0.2567 | 134 | 0.2142 | 1798 | 1932 | 91 | 2.3752-2.4703 | 0.2368 | 135 | 0.214 | 1833 | 1968 | 93 | 2.4703-2.5826 | 0.2538 | 131 | 0.2109 | 1913 | 2044 | 95 | 2.5826-2.7187 | 0.2283 | 141 | 0.1993 | 1886 | 2027 | 96 | 2.7187-2.889 | 0.2398 | 140 | 0.216 | 1936 | 2076 | 97 | 2.889-3.1119 | 0.262 | 143 | 0.2015 | 1928 | 2071 | 97 | 3.1119-3.4247 | 0.2417 | 140 | 0.1926 | 1938 | 2078 | 97 | 3.4247-3.9195 | 0.2076 | 147 | 0.1706 | 1945 | 2092 | 98 | 3.9195-4.9354 | 0.2016 | 144 | 0.157 | 1951 | 2095 | 98 | 4.9354-32.3884 | 0.2154 | 147 | 0.1942 | 1956 | 2103 | 96 |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION 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) |
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1 | 4.2777 | -0.6771 | 0.1919 | 2.7777 | 0.3841 | 1.8146 | -0.265 | -0.059 | 0.0104 | 0.0525 | 0.2618 | 0.2069 | -0.0238 | 0.0764 | 0.0595 | 0.0369 | 0.007 | -0.0336 | 0.0563 | -0.0198 | 0.1488 | -6.5411 | 17.6509 | 23.3176 | 2 | 2.0518 | -1.0748 | 0.1327 | 1.0047 | -0.5321 | 2.4389 | 0.1148 | 0.4303 | -0.2108 | -0.3051 | -0.1194 | -0.0302 | 0.2009 | 0.0275 | -0.0213 | 0.15 | 0.0119 | 0.0023 | 0.179 | -0.0441 | 0.1248 | 4.6997 | 13.1496 | 19.2073 | 3 | 2.8679 | 0.1893 | -0.103 | 3.8681 | -0.2869 | 2.1867 | 0.2771 | 0.6353 | -0.1244 | -1.2595 | -0.0419 | 1.6188 | -0.0676 | 0.0062 | 0.6131 | 0.0817 | 0.0005 | 0.1096 | 0.2747 | -0.0649 | -0.4142 | -4.8522 | 16.216 | 14.0153 | 4 | 2.253 | 1.2035 | -0.4291 | 2.6142 | -1.1231 | 1.5788 | 0.0798 | -0.1367 | 0.181 | -0.0369 | -0.1159 | -0.017 | -0.0714 | 0.0084 | 0.0173 | 0.1946 | -0.0718 | -0.005 | 0.1414 | 0.0103 | 0.3028 | -25.6901 | 5.2192 | 33.0597 | 5 | 1.5571 | -0.3514 | -0.2326 | 1.6018 | -0.7188 | 2.3294 | -0.3339 | 0.6255 | 0.1306 | -0.58 | 0.3376 | 0.1058 | -0.1088 | -0.5594 | 0.0477 | 0.4226 | -0.1326 | -0.1156 | 0.3505 | 0.1107 | 0.282 | -34.8555 | 4.1771 | 20.4839 | 6 | 2.8773 | 1.8229 | -1.7851 | 1.5312 | -0.8799 | 1.6958 | -0.1538 | -0.0005 | -0.2327 | -0.2068 | -0.0714 | -0.2258 | 0.2561 | 0.0884 | 0.1155 | 0.1764 | -0.0447 | -0.0266 | 0.1398 | -0.02 | 0.2755 | -32.8319 | -10.6605 | 35.8299 | 7 | 3.0495 | 1.2846 | -0.1279 | 3.7031 | -0.4705 | 3.2523 | -0.1046 | 0.3499 | 0.121 | -0.9974 | 0.1956 | -0.3522 | 0.1123 | 0.1605 | 0.0887 | 0.266 | -0.0585 | 0.0267 | 0.2194 | 0.0232 | 0.2176 | -27.272 | 4.3296 | 23.4958 | 8 | 4.3041 | -0.0958 | -0.0046 | 3.9715 | 0.2713 | 2.4136 | 0.0352 | -0.0598 | -0.8801 | -0.1759 | -0.0738 | -0.4761 | 0.1354 | 0.4025 | -0.0205 | 0.284 | -0.0728 | -0.0613 | 0.1789 | 0.0187 | 0.3902 | -24.9213 | -7.7134 | 41.5356 | 9 | 3.0303 | 0.5475 | -1.7794 | 1.1154 | 0.2707 | 2.1188 | -0.5077 | -0.2505 | 0.1451 | -0.2288 | -0.3403 | 0.8663 | 0.3591 | -0.7265 | -0.8881 | 0.5228 | -0.0669 | 0.3667 | 0.5476 | -0.11 | 0.7233 | -45.795 | -2.9782 | 54.5933 | 10 | 1.4432 | 0.9812 | -1.3625 | 0.7187 | -1.0234 | 1.4798 | 0.0185 | -0.4015 | 0.3278 | 0.1921 | 0.0291 | 0.3948 | 0.2319 | -0.3566 | -0.3586 | 0.601 | -0.2257 | 0.1757 | 0.632 | 0.0327 | 0.3894 | -41.9997 | -9.7604 | 61.4681 | 11 | 2.0013 | -0.149 | 0.5183 | 1.22 | -0.2265 | 3.0547 | -0.3901 | -0.4945 | 0.6986 | 0.9367 | -0.3589 | 0.6933 | -1.0204 | -0.0224 | -0.5573 | 0.5971 | -0.0692 | 0.1917 | 0.388 | -0.2854 | 0.284 | -34.2045 | 4.3112 | 54.2598 | 12 | 1.1994 | -0.2962 | -0.3206 | 2.6357 | -1.3018 | 2.3669 | 0.1935 | -0.7522 | 0.347 | 0.4935 | -0.1986 | -0.0575 | -0.864 | 0.8024 | 0.0723 | 0.4496 | -0.2201 | 0.011 | 0.2365 | -0.0974 | 0.263 | -25.5542 | 9.549 | 41.7239 | 13 | 2.3064 | 0.6313 | 0.3945 | 1.4592 | 0.766 | 0.4961 | -0.042 | -1.1809 | -0.2158 | 0.4838 | -0.0633 | -0.0833 | 0.0377 | 0.4693 | -0.0555 | 0.5265 | -0.1869 | -0.0361 | 0.5451 | -0.0393 | 0.1402 | -25.7164 | -1.9134 | 55.8953 | 14 | 1.213 | -0.0904 | -1.5109 | 5.7442 | 2.0242 | 3.6704 | -0.0131 | 0.2057 | -0.1928 | -0.2295 | -0.0196 | 0.595 | -0.156 | -0.6688 | -0.2503 | 0.3735 | -0.1702 | 0.0174 | 0.3823 | 0.0558 | 0.2022 | -42.513 | -11.5559 | 48.2094 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 132 through 170 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 171 through 219 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 220 through 251 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 132 through 170 )B0 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 171 through 193 )B0 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 194 through 218 )B0 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 219 through 251 )B0 | 8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 133 through 160 )C0 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 161 through 169 )C0 | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 170 through 179 )C0 | 11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 180 through 193 )C0 | 12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 194 through 219 )C0 | 13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 220 through 242 )C | | | | | | | | | | | | | | | | | | | | | | | | | |
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