Software | Name | Classification |
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XDS | data scalingXSCALE | data scalingPHASER | phasingARP | model building Coot | model buildingPHENIX | refinementPDB_EXTRACT | data extractionXDS | data reduction | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3PFT Resolution: 1.8→37.812 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.98 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2153 | 1427 | 5.02 % | Random selection |
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Rwork | 0.1788 | 27018 | - | - |
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obs | 0.1806 | 28445 | 99.75 % | - |
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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: 98.74 Å2 / Biso mean: 36.0889 Å2 / Biso min: 14.77 Å2 |
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Refinement step | Cycle: final / Resolution: 1.8→37.812 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2016 | 0 | 13 | 125 | 2154 |
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Biso mean | - | - | 55.49 | 41.48 | - |
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Num. residues | - | - | - | - | 279 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 2129 | X-RAY DIFFRACTION | f_angle_d0.993 | 2932 | X-RAY DIFFRACTION | f_chiral_restr0.049 | 367 | X-RAY DIFFRACTION | f_plane_restr0.004 | 378 | X-RAY DIFFRACTION | f_dihedral_angle_d11.695 | 754 | | | | | |
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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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1.8001-1.8644 | 0.2503 | 128 | 0.2035 | 2642 | X-RAY DIFFRACTION | 100 | 1.8644-1.939 | 0.2511 | 134 | 0.1954 | 2643 | X-RAY DIFFRACTION | 100 | 1.939-2.0273 | 0.2389 | 125 | 0.1851 | 2631 | X-RAY DIFFRACTION | 99 | 2.0273-2.1342 | 0.2714 | 149 | 0.1896 | 2635 | X-RAY DIFFRACTION | 100 | 2.1342-2.2679 | 0.2023 | 135 | 0.1869 | 2679 | X-RAY DIFFRACTION | 100 | 2.2679-2.4429 | 0.2295 | 132 | 0.1902 | 2685 | X-RAY DIFFRACTION | 100 | 2.4429-2.6887 | 0.2175 | 157 | 0.1874 | 2671 | X-RAY DIFFRACTION | 100 | 2.6887-3.0776 | 0.2332 | 150 | 0.1972 | 2718 | X-RAY DIFFRACTION | 100 | 3.0776-3.8769 | 0.2242 | 156 | 0.1653 | 2780 | X-RAY DIFFRACTION | 100 | 3.8769-50 | 0.1814 | 161 | 0.1664 | 2934 | X-RAY DIFFRACTION | 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 | 3.3691 | 1.021 | -0.947 | 1.9917 | -0.8008 | 3.1242 | -0.3697 | 0.7275 | -0.2893 | -0.7105 | 0.5851 | -0.1881 | 0.4368 | -0.4966 | -0.1292 | 0.5022 | -0.1476 | 0.0598 | 0.3564 | -0.0321 | 0.2721 | 18.7154 | -2.3569 | 32.416 | 2 | 5.036 | 0.5412 | -4.2299 | 1.2915 | -0.0509 | 9.4567 | -0.0632 | -0.0662 | -0.0542 | 0.1774 | 0.075 | 0.1446 | -0.2317 | -0.7369 | 0.0355 | 0.1917 | 0.0616 | -0.0099 | 0.2394 | 0.0454 | 0.1862 | 16.9693 | 3.9894 | 44.7058 | 3 | 5.6549 | 1.3735 | -0.5305 | 2.3209 | 0.5046 | 6.4228 | -0.2226 | 0.3835 | 0.2275 | 0.3341 | 0.2103 | 0.2851 | -0.6925 | -1.0127 | 0.0304 | 0.3612 | 0.1388 | 0.0257 | 0.2571 | 0.1038 | 0.1987 | 15.7076 | 8.8364 | 42.3934 | 4 | 5.0764 | 1.5649 | 1.1091 | 3.1831 | 3.1479 | 3.4381 | -0.0351 | 0.2864 | -0.5031 | -0.7763 | 0.3553 | -0.1066 | -0.1858 | 0.1755 | -0.3648 | 0.3284 | 0.0474 | -0.0016 | 0.1712 | -0.0112 | 0.2182 | 20.6111 | -3.8056 | 42.507 | 5 | 2.6736 | 0.4246 | 0.0216 | 1.4409 | 1.25 | 7.1527 | 0.1056 | -0.1447 | -0.1575 | 0.2763 | -0.0251 | -0.0935 | 0.3628 | -0.276 | -0.112 | 0.2107 | 0.0162 | -0.0174 | 0.16 | 0.0196 | 0.1982 | 19.5317 | -0.8697 | 51.334 | 6 | 7.179 | -1.2695 | 1.6953 | 4.0249 | -0.0613 | 8.2874 | -0.1764 | -0.0167 | 0.1826 | -0.0716 | 0.212 | 0.0161 | -1.0376 | -0.6262 | -0.0659 | 0.2383 | -0.0109 | 0.0765 | 0.1945 | 0.0025 | 0.1764 | 20.298 | 8.8919 | 39.3894 | 7 | 3.3464 | -0.225 | 4.2652 | 0.3645 | -1.2804 | 7.9427 | -0.9748 | -1.4696 | -0.6735 | 0.5117 | 0.996 | -0.0812 | 0.81 | 0.1794 | 0.0356 | 0.7832 | 0.3428 | 0.0606 | 0.6894 | 0.0791 | 0.5803 | 32.758 | -0.3578 | 38.0103 | 8 | 1.9909 | 0.3841 | -0.3664 | 1.6589 | 2.0907 | 3.0622 | 0.0744 | 0.0125 | 0.2163 | -0.4378 | -0.0069 | -0.1254 | 0.108 | -0.1308 | -0.0436 | 0.1779 | -0.0129 | 0.0382 | 0.1815 | 0.0414 | 0.2199 | 29.0688 | 8.5795 | 15.074 | 9 | 2.7537 | 0.9172 | -2.2147 | 4.7914 | -2.52 | 3.2012 | -0.335 | 0.1572 | -0.0489 | -0.3965 | 0.021 | -0.3258 | -0.0189 | -0.2037 | 0.1968 | 0.214 | -0.08 | -0.0201 | 0.2213 | -0.0259 | 0.1443 | 28.1637 | 8.775 | 19.1318 | 10 | 3.0204 | 3.4782 | -1.0627 | 7.9098 | -1.2636 | 5.9436 | 0.0868 | 0.0255 | -0.2015 | 0.0066 | -0.0376 | 0.065 | 0.1867 | -0.6093 | -0.1263 | 0.162 | -0.0216 | 0.0432 | 0.2081 | -0.0101 | 0.1232 | 22.3666 | 6.6269 | 26.0443 | 11 | 6.759 | 1.966 | 4.7906 | 4.5012 | 2.753 | 4.3659 | -0.645 | -0.1744 | 0.4249 | -0.3738 | 0.1835 | 0.0135 | -1.2245 | -0.1075 | 0.4958 | 0.4231 | -0.0068 | 0.006 | 0.2668 | 0.0444 | 0.2305 | 27.9524 | 17.4649 | 17.9413 | 12 | 6.3677 | -4.568 | 3.9936 | 3.5718 | -4.0389 | 7.6106 | -0.4435 | -0.5429 | -0.1324 | 0.2355 | 0.4798 | -0.3046 | 0.279 | -0.0242 | -0.0271 | 0.2587 | 0.0472 | -0.0248 | 0.2152 | -0.0007 | 0.249 | 31.7683 | 0.6855 | 21.7832 | 13 | 2.2784 | -3.2111 | 3.1094 | 5.0057 | -4.8567 | 4.6708 | 0.1652 | 0.7197 | 0.0769 | -0.0578 | -0.4191 | -0.1568 | -0.4607 | 1.0862 | 0.3207 | 0.3004 | 0.0535 | 0.0505 | 0.4314 | 0.0099 | 0.3369 | 39.6079 | 1.6821 | 17.8163 | 14 | 6.6694 | -2.0032 | 0.9644 | 5.5241 | 0.4079 | 7.9644 | 0.1927 | 0.4528 | 0.1091 | 0.047 | -0.1331 | -0.2502 | 0.1562 | 0.5839 | -0.0737 | 0.1672 | 0.0083 | -0.0011 | 0.1786 | 0.0072 | 0.1589 | 28.791 | 4.0268 | 8.6298 | 15 | 2.3048 | -0.2982 | -1.6901 | 6.8318 | 4.1967 | 9.4441 | -0.2257 | -0.0735 | -0.1376 | -0.0434 | 0.2372 | 0.2392 | 0.1621 | -1.0644 | 0.1267 | 0.1857 | -0.0403 | -0.024 | 0.3274 | 0.048 | 0.1827 | 21.5187 | 4.3412 | 16.348 | 16 | 8.0085 | 1.5548 | 1.6899 | 5.211 | 2.1 | 2.5377 | 0.0467 | 0.4665 | 0.9027 | 0.1011 | -0.1095 | 0.2143 | -0.9058 | 0.2401 | -0.1524 | 0.3596 | -0.0029 | 0.0372 | 0.2921 | 0.0058 | 0.1904 | 25.2953 | 15.9425 | 30.1398 | 17 | 3.0234 | -0.0045 | -0.4668 | 6.3993 | -0.1461 | 2.8809 | -0.1201 | -0.0316 | -0.1193 | -0.605 | 0.0237 | 0.4268 | -0.2528 | -0.7655 | 0.1555 | 0.1486 | -0.0346 | 0.0176 | 0.2645 | 0.0402 | 0.167 | 21.2494 | 6.8491 | 21.7239 | 18 | 9.9045 | 0.6879 | -0.4552 | 6.8272 | 1.7122 | 9.0886 | -0.0859 | 0.1077 | -1.189 | -0.3758 | -0.2614 | 1.019 | 1.2678 | 0.1563 | 0.2339 | 0.9686 | 0.0136 | -0.1329 | 0.2852 | -0.0349 | 0.5705 | 28.1797 | -9.5924 | 15.974 |
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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 8 through 31 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 32 through 47 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 48 through 72 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 73 through 83 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 84 through 123 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 124 through 145 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 12 through 22 )B0 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 23 through 31 )B0 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 32 through 47 )B0 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 48 through 58 )B0 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 59 through 72 )B0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 73 through 83 )B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 84 through 94 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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