Software | Name | Version | Classification |
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PHENIX | 1.18.2refinementXSCALE | | data scalingXDS | | data reductionMOLREP | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→31.67 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.57 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2043 | 360 | 5 % |
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Rwork | 0.1565 | - | - |
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obs | 0.1589 | 7194 | 99.89 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 3.09→31.67 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1887 | 0 | 60 | 7 | 1954 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.014 | 1999 | X-RAY DIFFRACTION | f_angle_d2.308 | 2711 | X-RAY DIFFRACTION | f_dihedral_angle_d6.942 | 290 | X-RAY DIFFRACTION | f_chiral_restr0.126 | 311 | X-RAY DIFFRACTION | f_plane_restr0.028 | 347 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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3.09-3.53 | 0.2326 | 119 | 0.1789 | 2259 | X-RAY DIFFRACTION | 100 | 3.54-4.45 | 0.2145 | 120 | 0.1527 | 2269 | X-RAY DIFFRACTION | 100 | 4.46-31.67 | 0.1892 | 121 | 0.1514 | 2306 | X-RAY DIFFRACTION | 100 |
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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 | 0.0007 | 0.0887 | 0.0524 | 0.8213 | 0.3396 | 0.1285 | -0.1246 | 0.7365 | 0.6911 | -0.2069 | 0.6032 | 0.3033 | -0.5012 | 1.1902 | -0.007 | 0.4245 | 0.0081 | 0.0157 | 0.6918 | -0.0969 | 0.5242 | 24.1697 | 23.1355 | 15.3795 | 2 | 0.6608 | -0.2574 | -0.7236 | 1.1649 | 0.4079 | 0.8043 | -0.9142 | 0.0939 | -0.2125 | 1.3806 | 0.3689 | 0.6851 | -0.0665 | 0.7898 | -0.0276 | 0.6143 | -0.0955 | -0.0706 | 0.7387 | -0.1057 | 0.869 | 4.0829 | 22.3757 | 6.6982 | 3 | 0.4176 | 0.0415 | -0.347 | 0.4688 | 0.3602 | 0.8236 | 0.2817 | 0.433 | -0.2442 | 0.4343 | -0.1746 | 0.2122 | 0.3383 | -0.1514 | -0.0001 | 0.5149 | 0.0209 | 0.0521 | 0.5449 | 0.1011 | 0.4888 | 15.6651 | 13.2976 | 11.9046 | 4 | 1.4659 | 1.9046 | 0.9843 | 2.4455 | 1.0866 | 2.1077 | 0.418 | -0.5682 | 0.9705 | -0.5028 | -0.4594 | -0.2068 | 0.1105 | 0.3204 | -0.0015 | 0.3883 | 0.1962 | 0.0095 | 0.7542 | 0.0494 | 0.4756 | 16.3001 | 22.4427 | 15.0553 | 5 | 0.4975 | 0.1315 | -0.2705 | 0.2593 | 0.1073 | 0.2698 | -0.3852 | -1.358 | 0.2729 | 0.4181 | 0.3 | 0.6559 | 0.2879 | -1.094 | -0.0001 | 0.6014 | 0.1012 | -0.0456 | 0.8218 | -0.1441 | 0.5951 | 17.865 | 28.5633 | 20.8709 | 6 | 0.1084 | -0.16 | -0.0235 | 2.7139 | 0.7515 | 0.2347 | -0.1876 | -0.7991 | 0.5712 | -0.2303 | -0.625 | -0.0466 | -0.329 | 0.4207 | -0.2209 | 0.2989 | -0.1009 | 0.0088 | 0.749 | -0.0291 | 0.4574 | 23.1152 | 25.6643 | 10.4514 | 7 | 1.4752 | -1.0555 | -1.1143 | 1.354 | 1.4056 | 1.409 | -0.1934 | 0.5046 | 0.5965 | -0.4254 | 0.4594 | 0.1342 | -1.3657 | 1.1578 | 0.0506 | 0.7096 | -0.0672 | -0.0312 | 0.4682 | 0.0051 | 0.3912 | 19.699 | 35.6246 | 10.7838 | 8 | 2.0543 | -1.0575 | -0.1653 | 0.5452 | 0.0943 | 0.0079 | -0.1506 | 0.2371 | 0.3029 | 0.1545 | 0.098 | 0.2475 | -0.0045 | 1.2415 | -0 | 0.5096 | -0.1233 | 0.0566 | 0.6993 | 0.0699 | 0.6878 | 25.8189 | 25.7993 | 4.9398 | 9 | 1.2182 | -0.8525 | -0.9885 | 0.585 | 0.6837 | 0.7955 | 0.4246 | -0.5951 | -0.6089 | 0.1441 | -0.3021 | -0.5188 | 0.7199 | 0.5074 | 0.0001 | 0.6188 | 0.1264 | 0.0363 | 0.4404 | 0.0408 | 0.5542 | 18.7955 | 7.5076 | -6.042 | 10 | 0.7704 | -0.1109 | 1.1617 | 0.0031 | -0.1366 | 1.4969 | 0.3929 | -0.1564 | 0.1757 | 0.7819 | -0.7999 | 0.507 | 0.7691 | -0.0891 | -0.0039 | 0.6384 | -0.0434 | 0.0193 | 0.4262 | -0.0363 | 0.5268 | 11.5979 | 19.1837 | -12.551 | 11 | 0.8278 | 0.2146 | 0.6766 | 0.1904 | 0.0878 | 0.6116 | -0.228 | 0.3814 | 0.3902 | -0.3801 | 0.4424 | -0.1172 | -0.6406 | 0.7026 | 0.0002 | 0.6032 | 0.0648 | 0.1041 | 0.5558 | 0.024 | 0.5325 | 21.1155 | 18.7815 | -12.9159 | 12 | 1.3043 | 0.8797 | 0.384 | 1.0933 | 0.7912 | 2.3136 | -0.2004 | 0.084 | 0.1444 | -0.9198 | 0.1156 | 0.9436 | -0.008 | 0.1869 | -0.0033 | 0.8017 | 0.0852 | 0.0287 | 0.4394 | 0.032 | 0.5925 | 11.9498 | 18.1045 | -16.1025 | 13 | 0.47 | -0.2455 | -0.3218 | 0.4079 | 0.373 | 0.3648 | 0.7944 | 1.2916 | 0.86 | -1.7225 | -0.5344 | -0.0738 | -1.0565 | -0.4312 | 0.0219 | 0.8532 | 0.1533 | -0.1906 | 0.6643 | -0.0726 | 0.6473 | 5.8158 | 16.5587 | -21.8437 | 14 | 3.5302 | -1.1057 | 2.1933 | 1.0341 | -1.4461 | 2.0431 | 0.1782 | -0.9207 | 0.274 | -0.6496 | 0.205 | 0.0382 | 0.5216 | -1.3664 | 0.1691 | 0.662 | -0.0455 | -0.0584 | 0.3576 | 0.0662 | 0.4661 | 4.9388 | 14.4765 | -8.8224 | 15 | 0.2207 | -0.2401 | 0.5594 | 0.3528 | -0.4403 | 0.7644 | 0.5841 | -0.3567 | -0.4844 | 0.1153 | 0.1201 | -0.4172 | 1.327 | -0.4776 | 0.126 | 0.6451 | -0.181 | 0.0162 | 0.5577 | 0.0721 | 0.3941 | 2.6596 | 9.9661 | -11.4645 | 16 | 0.6355 | -0.6735 | 0.7723 | 0.9551 | -0.7177 | 0.9559 | -0.0466 | 0.753 | -0.1101 | -0.5044 | 0.2285 | 0.0989 | 0.5935 | 1.1701 | 0.0025 | 0.4991 | 0.142 | 0.0232 | 0.667 | 0.0482 | 0.4943 | 26.8812 | 15.5807 | 5.0301 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 1 through 8 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 9 through 14 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 15 through 30 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 31 through 47 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 48 through 57 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 58 through 73 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 74 through 118 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 119 through 129 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 130 through 143 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 1 through 14 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 15 through 30 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 31 through 47 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 48 through 57 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 58 through 83 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 84 through 129 )16 | X-RAY DIFFRACTION | 16 | chain 'B' | | | | | | | | | | | | | | | |
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