Software | Name | Version | Classification |
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PHENIX | (1.10.1_2155: ???)refinementHKL-2000 | | data scalingPHASER | | phasing | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5y7r Resolution: 2.44→29.472 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 42.89
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2855 | 1108 | 5 % |
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Rwork | 0.2176 | - | - |
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obs | 0.2211 | 22174 | 97.15 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Refinement step | Cycle: LAST / Resolution: 2.44→29.472 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4436 | 0 | 68 | 41 | 4545 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 4610 | X-RAY DIFFRACTION | f_angle_d1.086 | 6286 | X-RAY DIFFRACTION | f_dihedral_angle_d7.662 | 3774 | X-RAY DIFFRACTION | f_chiral_restr0.061 | 738 | X-RAY DIFFRACTION | f_plane_restr0.009 | 817 | | | | | |
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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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2.4402-2.5512 | 0.3365 | 121 | 0.2809 | 2130 | X-RAY DIFFRACTION | 81 | 2.5512-2.6857 | 0.3769 | 147 | 0.2801 | 2662 | X-RAY DIFFRACTION | 100 | 2.6857-2.8538 | 0.3502 | 141 | 0.2822 | 2657 | X-RAY DIFFRACTION | 100 | 2.8538-3.0739 | 0.3507 | 128 | 0.2671 | 2690 | X-RAY DIFFRACTION | 100 | 3.0739-3.3829 | 0.3341 | 141 | 0.2447 | 2682 | X-RAY DIFFRACTION | 100 | 3.3829-3.8715 | 0.2907 | 156 | 0.2083 | 2680 | X-RAY DIFFRACTION | 100 | 3.8715-4.8741 | 0.2386 | 127 | 0.179 | 2754 | X-RAY DIFFRACTION | 100 | 4.8741-29.474 | 0.2395 | 147 | 0.1904 | 2811 | X-RAY DIFFRACTION | 98 |
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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 | 1.8038 | 0.9031 | -1.7702 | 1.0053 | -1.507 | 2.4343 | -0.0256 | -0.0024 | -0.0434 | -0.3165 | -0.1216 | -0.0907 | 0.9508 | 1.2241 | 0.13 | 0.4585 | 0.098 | -0.0721 | 0.4598 | -0.1006 | 0.366 | -13.6194 | -8.0394 | -27.336 | 2 | 8.2902 | -4.7534 | -5.1793 | 7.2528 | 5.092 | 6.2263 | -0.4513 | -0.1646 | -0.0602 | 0.8241 | -0.0265 | 0.3036 | 0.0339 | -0.2776 | 0.4336 | 0.5161 | -0.0303 | 0.0044 | 0.4527 | -0.0414 | 0.3566 | -24.8082 | -7.5327 | -5.3604 | 3 | 0.9424 | 1.4136 | 0.0349 | 7.078 | -0.2121 | 4.7062 | -0.3112 | -0.7957 | 1.0861 | -0.0321 | 0.0955 | 1.4596 | -0.995 | -1.0418 | 0.145 | 0.5571 | 0.0935 | -0.0352 | 0.4823 | -0.2051 | 0.8104 | -34.0397 | 6.7309 | -10.9863 | 4 | 8.5339 | 3.4853 | -5.5343 | 8.6454 | -3.4252 | 4.1787 | 0.0154 | -0.5364 | -0.7722 | 0.4636 | -0.6851 | -0.7965 | -1.1652 | 0.0202 | 0.5641 | 0.4126 | 0.067 | -0.0661 | 0.3061 | -0.0709 | 0.3528 | -11.0855 | -0.4567 | -14.2393 | 5 | 0.9481 | 1.8692 | -0.3852 | 3.5806 | -1.0762 | 1.705 | -0.2401 | -0.0105 | 0.3599 | -0.5326 | 0.1787 | 0.7092 | 0.3638 | -0.3338 | 0.0642 | 0.5178 | -0.0083 | -0.1507 | 0.3949 | -0.107 | 0.4341 | -22.6874 | 6.8408 | -24.0445 | 6 | 4.8658 | 0.3622 | 0.364 | 2.1371 | 1.1769 | 5.9137 | -0.3041 | 1.3616 | 0.0604 | -0.7805 | 0.4979 | 0.5525 | -0.5513 | -0.5828 | -0.2509 | 0.6231 | -0.118 | -0.223 | 0.6737 | -0.037 | 0.4586 | -28.2091 | -2.9937 | -32.5408 | 7 | 2.6344 | 0.1764 | -0.5757 | 1.7242 | -1.7295 | 1.7512 | -0.1578 | 0.1331 | -0.0318 | -0.4629 | 0.1545 | 0.4954 | 0.0845 | -0.4208 | 0.0349 | 0.5561 | 0.0657 | -0.1379 | 0.3527 | -0.1129 | 0.4492 | -26.7893 | -4.8139 | -22.7859 | 8 | 3.3458 | -0.2739 | -1.4674 | 3.3249 | -2.1457 | 2.3223 | 0.086 | -0.2999 | 0.2114 | -0.0318 | -0.1575 | 0.5063 | 0.0748 | -0.2883 | 0.1096 | 0.3145 | -0.0507 | -0.0699 | 0.3601 | -0.1414 | 0.3628 | -14.3862 | 10.2854 | -7.178 | 9 | 1.7842 | 1.6007 | -2.1316 | 5.1896 | -2.4387 | 2.8231 | 0.6351 | -0.7274 | 0.2779 | 0.0453 | -0.5792 | -0.2285 | -0.3963 | 0.0758 | -0.054 | 0.3107 | 0.0017 | -0.1379 | 0.4734 | -0.13 | 0.3902 | -5.7803 | 18.7036 | -14.2027 | 10 | 0.8797 | 0.7827 | -1.3478 | 2.3521 | -3.9013 | 6.4626 | 1.362 | -1.2459 | -0.0476 | 2.819 | -1.2465 | -0.3824 | -0.9435 | 1.1893 | 0.0408 | 1.0743 | -0.3241 | -0.137 | 1.1231 | 0.003 | 0.4638 | -5.7135 | 13.1112 | -0.7254 | 11 | 5.0494 | 0.2336 | 2.0987 | 2.4454 | -4.2964 | 9.3643 | 0.0867 | 0.3201 | 0.3146 | -0.3048 | 0.1429 | 0.7989 | -0.1418 | -0.0957 | -0.2172 | 0.9161 | 0.1086 | -0.4424 | 0.5055 | -0.0489 | 0.9389 | -19.7499 | 44.7477 | -27.3326 | 12 | 7.8024 | -4.8425 | 5.3794 | 8.3637 | -4.7823 | 6.7282 | -0.8659 | -1.488 | 0.9519 | 1.2741 | 0.5297 | 0.0339 | -1.5451 | -0.1525 | 0.3662 | 0.6597 | -0.1052 | 0.0329 | 0.7819 | -0.3626 | 0.6413 | -8.5529 | 44.2431 | -5.3544 | 13 | 3.944 | 1.2876 | -3.3943 | 0.5413 | -1.0277 | 2.9584 | 0.5609 | -0.1025 | -0.0878 | 0.3683 | -0.3684 | -0.3425 | -0.7465 | -0.018 | -0.119 | 0.4396 | -0.0465 | -0.1528 | 0.711 | -0.1971 | 0.5054 | 0.6397 | 29.959 | -10.9906 | 14 | 7.3689 | 2.0133 | 2.2145 | 2.1805 | 0.6283 | 3.5 | 0.3332 | -0.4687 | 0.6977 | -0.3084 | -0.5528 | 1.1076 | -0.0831 | -0.5719 | 0.2237 | 0.4563 | 0.0418 | -0.2059 | 0.4845 | -0.1354 | 0.7732 | -19.4388 | 34.2594 | -15.9566 | 15 | 0.7435 | 1.5279 | -0.4685 | 3.3473 | -0.3475 | 0.7076 | 0.0085 | -0.1497 | 0.1901 | -0.5859 | -0.166 | 0.2249 | 0.3365 | -0.1496 | 0.1658 | 0.6624 | 0.1514 | -0.2097 | 0.4685 | -0.0309 | 0.4386 | -8.3746 | 29.552 | -26.7307 | 16 | 5.9622 | 2.1624 | -0.4625 | 5.1867 | -0.608 | 5.908 | -0.1347 | -0.2177 | -0.3095 | -1.1402 | -0.3228 | -0.155 | -0.6782 | 0.0745 | 0.5415 | 0.6892 | 0.1362 | -0.248 | 0.4379 | -0.0235 | 0.5039 | -5.1351 | 39.649 | -32.512 | 17 | 3.8343 | 0.287 | -0.8793 | 2.4027 | -1.4892 | 1.0972 | -0.0604 | -0.0907 | 0.414 | 0.002 | -0.0322 | 0.2982 | -0.3216 | 0.1192 | 0.0897 | 0.5477 | 0.0255 | -0.1459 | 0.4312 | -0.1383 | 0.4793 | -6.5791 | 41.4841 | -22.7824 | 18 | 5.1078 | -1.9094 | -0.5981 | 6.0588 | -2.4221 | 2.9516 | 0.1909 | -1.0252 | -0.0872 | 0.3994 | -0.2485 | 0.6299 | -0.1451 | -0.2805 | 0.0775 | 0.4638 | -0.0591 | 0.0289 | 0.6251 | -0.2235 | 0.5305 | -18.9813 | 26.4393 | -7.1871 | 19 | 6.8747 | 0.7723 | -1.1399 | 9.0222 | -5.6047 | 8.0996 | 0.3149 | 0.766 | -0.5536 | -0.105 | 0.8048 | 0.7736 | -0.6949 | -0.4689 | -0.9385 | 0.4664 | 0.1475 | -0.0622 | 0.5948 | -0.2047 | 0.6364 | -27.5864 | 17.973 | -14.2285 | 20 | 0.0212 | -0.3776 | -0.1159 | 6.9175 | 1.5787 | 1.2063 | -0.1855 | -0.4746 | 0.237 | 0.7185 | -0.1926 | 0.2431 | 0.105 | -0.0141 | -0.0379 | -0.0588 | 0.4412 | 0.2275 | 0.4871 | -0.56 | 1.2072 | -27.7206 | 23.5245 | -0.7197 |
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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 'B' and (resid 9 through 40 )2 | X-RAY DIFFRACTION | 2 | chain 'B' and (resid 41 through 56 )3 | X-RAY DIFFRACTION | 3 | chain 'B' and (resid 57 through 87 )4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 88 through 108 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 109 through 161 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 162 through 191 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 192 through 232 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 233 through 259 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 260 through 279 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 280 through 295 )11 | X-RAY DIFFRACTION | 11 | chain 'F' and (resid 9 through 40 )12 | X-RAY DIFFRACTION | 12 | chain 'F' and (resid 41 through 56 )13 | X-RAY DIFFRACTION | 13 | chain 'F' and (resid 57 through 87 )14 | X-RAY DIFFRACTION | 14 | chain 'F' and (resid 88 through 124 )15 | X-RAY DIFFRACTION | 15 | chain 'F' and (resid 125 through 161 )16 | X-RAY DIFFRACTION | 16 | chain 'F' | | | | | | | | | | | | | | | |
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