Software | Name | Classification |
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XDS | data reductionXSCALE | data scalingPHASER | phasing Coot | model buildingPHENIX | refinementPDB_EXTRACT | data extraction | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IXH Resolution: 1.85→43.339 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2175 | 1814 | 3.63 % | 0 |
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Rwork | 0.1702 | - | - | - |
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obs | 0.1719 | 49948 | 97.55 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 79.66 Å2 / Biso mean: 30.092 Å2 / Biso min: 10.29 Å2 |
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Refinement step | Cycle: final / Resolution: 1.85→43.339 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4684 | 0 | 12 | 610 | 5306 |
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Biso mean | - | - | 16.34 | 35.65 | - |
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Num. residues | - | - | - | - | 640 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 4852 | X-RAY DIFFRACTION | f_angle_d0.775 | 6650 | X-RAY DIFFRACTION | f_chiral_restr0.053 | 749 | X-RAY DIFFRACTION | f_plane_restr0.005 | 861 | X-RAY DIFFRACTION | f_dihedral_angle_d12.775 | 2790 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8501-1.9001 | 0.3009 | 155 | 0.24 | 3383 | 3538 | 91 | 1.9001-1.956 | 0.3017 | 169 | 0.2359 | 3476 | 3645 | 93 | 1.956-2.0191 | 0.3058 | 135 | 0.2266 | 3587 | 3722 | 95 | 2.0191-2.0913 | 0.2746 | 144 | 0.2059 | 3658 | 3802 | 97 | 2.0913-2.175 | 0.2636 | 139 | 0.2009 | 3721 | 3860 | 99 | 2.175-2.274 | 0.2579 | 142 | 0.1938 | 3737 | 3879 | 99 | 2.274-2.3939 | 0.2202 | 138 | 0.1806 | 3749 | 3887 | 99 | 2.3939-2.5438 | 0.2479 | 128 | 0.1829 | 3761 | 3889 | 99 | 2.5438-2.7402 | 0.2424 | 126 | 0.1793 | 3793 | 3919 | 99 | 2.7402-3.0159 | 0.2283 | 132 | 0.1783 | 3777 | 3909 | 100 | 3.0159-3.4522 | 0.2318 | 132 | 0.1584 | 3810 | 3942 | 99 | 3.4522-4.3487 | 0.1662 | 143 | 0.1426 | 3807 | 3950 | 99 | 4.3487-43.351 | 0.1575 | 131 | 0.1412 | 3875 | 4006 | 99 |
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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 | 0.9979 | -0.2705 | 1.2401 | 1.8505 | -1.8163 | 4.0321 | -0.2643 | -0.2648 | 0.0687 | 0.4404 | -0.0206 | 0.4308 | -0.3302 | -1.4379 | 0.1871 | 0.3339 | 0.0128 | 0.1306 | 0.5104 | -0.1208 | 0.44 | -11.9293 | 8.9311 | 43.3828 | 2 | 2.798 | -0.6365 | 1.9379 | 2.8391 | 0.4618 | 1.6596 | -0.1015 | -0.0165 | -0.4427 | 0.6972 | 0.2079 | 0.5743 | 0.3608 | -0.8639 | -0.0871 | 0.5117 | -0.1653 | 0.2208 | 0.6352 | 0.0508 | 0.5164 | -13.8836 | -3.052 | 51.2635 | 3 | 3.9513 | 0.8101 | -0.1615 | 2.6552 | 0.0817 | 3.236 | -0.0753 | 0.6155 | 0.2962 | -0.3885 | 0.124 | -0.0168 | -0.5176 | -0.3643 | -0.0571 | 0.273 | 0.0423 | -0.0037 | 0.2582 | 0.0503 | 0.1994 | -21.1236 | -20.3408 | -0.438 | 4 | 2.5562 | -0.0306 | 0.213 | 2.3594 | 0.8251 | 3.8976 | -0.0484 | 0.3818 | -0.5376 | -0.0554 | 0.0047 | 0.1322 | 0.5927 | -0.5302 | 0.0125 | 0.2357 | -0.0527 | 0.0103 | 0.2394 | -0.0739 | 0.2765 | -23.0047 | -35.6153 | 0.5541 | 5 | 2.104 | 0.0788 | -1.2967 | 0.5085 | 0.4255 | 2.6415 | 0.0165 | -0.1917 | 0.0054 | 0.0298 | 0.044 | -0.0129 | -0.0129 | -0.0296 | -0.059 | 0.144 | 0.0394 | -0.0163 | 0.1725 | 0.0326 | 0.1492 | -27.3584 | -24.1002 | 24.4685 | 6 | 0.8529 | -1.0851 | -0.7649 | 5.6334 | 4.4479 | 6.6471 | -0.177 | -0.3335 | -0.4171 | -0.0988 | 0.3477 | -0.5798 | 0.5331 | 1.1011 | -0.209 | 0.2685 | 0.0962 | 0.0471 | 0.4977 | 0.0704 | 0.3545 | -9.7468 | -30.8465 | 15.3361 | 7 | 2.0464 | -0.3588 | -0.6736 | 1.3433 | 0.9088 | 4.8577 | -0.0452 | 0.0568 | 0.0197 | -0.1157 | 0.0584 | -0.049 | -0.131 | 0.1625 | -0.0066 | 0.109 | 0.0095 | -0.0153 | 0.1146 | 0.0022 | 0.1746 | -13.3532 | -25.8116 | 5.8069 | 8 | 4.0383 | 2.2096 | 5.0744 | 3.5549 | 4.6181 | 9.3502 | 0.0449 | 0.1766 | -0.2758 | -0.2156 | -0.0091 | -0.045 | 0.0618 | 0.2241 | -0.0192 | 0.1763 | 0.0042 | 0.0296 | 0.1937 | -0.0565 | 0.2214 | -8.0084 | -33.5376 | -4.2175 | 9 | 3.8028 | -1.0562 | -0.327 | 1.493 | -0.7701 | 4.2244 | -0.2252 | -0.2607 | 0.6039 | 0.701 | -0.083 | 0.1593 | -0.3436 | -0.4594 | 0.2569 | 0.3776 | -0.0157 | 0.0632 | 0.2197 | -0.107 | 0.3714 | -3.9884 | 11.895 | 43.4638 | 10 | 4.4043 | -2.0918 | -1.2143 | 3.2556 | 1.4608 | 3.7898 | -0.169 | -0.413 | 0.1862 | 0.6366 | 0.0311 | 0.1118 | -0.1323 | 0.0306 | 0.1306 | 0.403 | -0.067 | 0.0462 | 0.1984 | -0.0378 | 0.2715 | 2.4051 | 6.198 | 45.6767 | 11 | 1.8191 | -0.1261 | -0.0804 | 0.9182 | 0.4534 | 1.2151 | -0.0485 | 0.022 | -0.2565 | 0.2076 | -0.0441 | 0.2143 | 0.4096 | -0.2664 | 0.0621 | 0.26 | -0.0681 | 0.0331 | 0.1843 | -0.0453 | 0.2753 | -0.6469 | 0.9192 | 30.4682 | 12 | 3.336 | 0.4089 | 1.7666 | 1.7034 | -0.3971 | 5.4969 | -0.0081 | 0.7007 | 0.1323 | -0.1922 | -0.1771 | 0.0936 | 0.2724 | 0.2969 | 0.1869 | 0.1996 | 0.0143 | -0.0308 | 0.353 | -0.0041 | 0.1546 | 6.2315 | 5.6953 | 6.7452 | 13 | 2.2078 | 0.5929 | 0.9756 | 1.3583 | -0.4636 | 0.8999 | -0.0084 | 0.3192 | -0.376 | 0.1312 | -0.1601 | 0.1324 | 0.7596 | -0.0007 | 0.0959 | 0.3549 | -0.046 | 0.0358 | 0.2052 | -0.088 | 0.2456 | 5.3594 | -4.3204 | 23.8071 | 14 | 2.7365 | -1.1272 | -1.1889 | 1.8749 | 0.0556 | 4.8837 | 0.0197 | 0.1155 | 0.2188 | 0.1106 | -0.1102 | 0.0998 | -0.2609 | 0.057 | 0.0876 | 0.1459 | -0.0381 | -0.0257 | 0.1672 | 0.0174 | 0.1962 | 5.6719 | 11.4354 | 24.8724 | 15 | 5.4138 | 1.5861 | 2.5468 | 2.5437 | -0.843 | 2.4106 | -0.0464 | 0.4286 | 0.0185 | -0.1951 | -0.0184 | 0.5179 | 0.1657 | -0.6475 | 0.1148 | 0.1901 | -0.0721 | -0.0309 | 0.4949 | -0.0418 | 0.2901 | -6.7764 | 7.5136 | 16.3413 | 16 | 1.5064 | 0.9862 | -0.5677 | 0.9785 | -0.0119 | 0.622 | -0.0018 | 0.0836 | -0.7122 | 0.1857 | -0.0025 | 0.5503 | 0.4468 | -0.7908 | -0.0105 | 0.3648 | -0.2418 | 0.1114 | 0.6055 | -0.1554 | 0.6476 | -13.298 | -2.5101 | 30.3522 | 17 | 0.4636 | -0.0589 | -0.2389 | 2.4985 | -0.3121 | 0.1593 | -0.2258 | 0.0945 | -0.288 | 0.3153 | 0.1037 | 0.4505 | 0.2937 | -0.3685 | -0.0706 | 0.2138 | -0.3182 | 0.123 | 0.3713 | -0.1496 | 0.3887 | -6.8915 | -1.4802 | 34.569 |
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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 'B' and (resid 287 through 317 )B287 - 317 | 2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 318 through 341 )B318 - 341 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 22 through 66 )A22 - 66 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 67 through 88 )A67 - 88 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 89 through 240 )A89 - 240 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 241 through 258 )A241 - 258 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 259 through 317 )A259 - 317 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 318 through 341 )A318 - 341 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 22 through 45 )B22 - 45 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 46 through 66 )B46 - 66 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 67 through 124 )B67 - 124 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 125 through 152 )B125 - 152 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 153 through 191 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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