Software | Name | Version | Classification |
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PHENIX | (1.10_2155: ???)refinementxia2 | | data reductionxia2 | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.561→90.56 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.83 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.284 | 336 | 4.87 % |
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Rwork | 0.1837 | - | - |
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obs | 0.1883 | 6901 | 99.84 % |
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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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Refinement step | Cycle: LAST / Resolution: 3.561→90.56 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3085 | 0 | 0 | 0 | 3085 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 3115 | X-RAY DIFFRACTION | f_angle_d0.545 | 4245 | X-RAY DIFFRACTION | f_dihedral_angle_d11.317 | 1860 | X-RAY DIFFRACTION | f_chiral_restr0.039 | 504 | X-RAY DIFFRACTION | f_plane_restr0.003 | 583 | | | | | |
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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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3.5611-4.4866 | 0.2492 | 173 | 0.2021 | 3216 | X-RAY DIFFRACTION | 100 | 4.4866-90.5895 | 0.3072 | 163 | 0.1742 | 3349 | 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 | 0.02 | 0.044 | 0.0269 | 0.0493 | 0.0584 | 0.0407 | 0.0306 | -0.4616 | -0.5749 | 0.8293 | -0.3789 | -0.0669 | -0.0122 | -0.3127 | 0.0008 | 1.618 | -0.3046 | 0.1228 | 1.1278 | 0.1164 | 1.3358 | -23.0616 | 45.4049 | -23.9633 | 2 | 1.06 | 0.6211 | -0.1565 | 0.6471 | -0.6656 | 0.769 | 0.1107 | 0.1764 | 0.423 | 0.0051 | -0.1046 | 0.2168 | -0.4551 | 0.2911 | 0.0001 | 0.9605 | -0.1819 | 0.01 | 0.7964 | 0.1387 | 0.7904 | -32.7243 | 37.0467 | -24.7077 | 3 | 0.5817 | 0.3747 | 0.0616 | 0.4875 | 0.2539 | 0.2056 | -0.2933 | 0.2661 | 1.0563 | 0.0104 | 0.4417 | -0.2179 | -0.2673 | 0.1057 | -0.0008 | 0.9405 | -0.1003 | 0.0374 | 0.691 | -0.0211 | 0.7994 | -40.4654 | 31.3922 | -22.5723 | 4 | 0.9996 | 0.5384 | -0.0502 | 0.4258 | -0.3625 | 0.3936 | 0.1288 | 0.2611 | -0.6227 | 0.1698 | 0.3059 | 0.2804 | -0.6508 | -0.0216 | 0.0007 | 0.8034 | -0.0438 | -0.0454 | 0.4482 | 0.0165 | 0.7788 | -41.0854 | 23.3302 | -19.4909 | 5 | 0.307 | 0.1636 | -0.1758 | 0.1281 | -0.2403 | 0.3753 | 0.0397 | 0.2069 | -0.0307 | -0.2445 | -0.0744 | -0.0541 | 0.2509 | -0.5477 | 0.0001 | 0.7022 | 0.0087 | -0.0662 | 0.6002 | -0.0318 | 0.5669 | -47.5333 | 25.839 | -21.3495 | 6 | 0.567 | 0.4927 | -0.1041 | 0.3848 | -0.0671 | 0.2805 | 0.1783 | -0.731 | -0.0688 | -0.2844 | -0.0002 | -0.4353 | 0.108 | -0.3324 | 0.0003 | 0.6907 | -0.059 | 0.0755 | 0.71 | 0.0432 | 0.7342 | -50.5592 | 21.6382 | -20.6619 | 7 | 0.3456 | 0.2252 | 0.3664 | 0.274 | 0.2095 | 0.4392 | -0.4879 | -0.2315 | 0.3567 | -0.8231 | -0.1823 | 1.2986 | -0.5718 | -0.4527 | -0.0537 | 0.7987 | 0.0419 | 0.1052 | 0.7142 | 0.0855 | 0.8629 | -56.3254 | 24.3861 | -16.8767 | 8 | 0.1384 | 0.1516 | 0.082 | 0.1445 | 0.0843 | 0.0397 | 0.0232 | 0.0681 | 0.2126 | -0.0859 | -0.2854 | 0.0758 | 0.189 | -0.5331 | 0.0001 | 0.6421 | 0.0738 | 0.0826 | 0.6105 | -0.0007 | 0.6435 | -56.7016 | 17.4174 | -19.7128 | 9 | 0.2808 | -0.29 | -0.083 | 0.3261 | -0.0166 | 0.2409 | 0.0371 | 0.5016 | 0.357 | -0.5827 | 0.0881 | -0.5697 | 0.208 | -0.6214 | 0.0001 | 0.9408 | -0.052 | 0.0681 | 0.8298 | 0.0624 | 0.6876 | -64.6473 | 11.4099 | -18.4494 | 10 | 0.6231 | 0.4448 | -0.2088 | 0.4387 | 0.4569 | 1.8175 | -0.2267 | 0.2484 | -0.8802 | 0.0856 | 0.4837 | -0.2365 | 0.7478 | 0.6216 | -1.3978 | 1.5443 | -0.0888 | -0.2107 | 0.7929 | -0.0187 | 1.0453 | -27.7178 | -5.2954 | -4.5101 | 11 | 0.4081 | 0.0621 | -0.0922 | 0.2936 | 0.0094 | 0.1295 | 0.5311 | 0.0674 | -0.5216 | -0.0446 | -0.2298 | 0.7704 | 1.0002 | -0.2677 | 0.0008 | 1.4252 | -0.1163 | -0.2385 | 0.7517 | 0.0797 | 1.0716 | -25.4659 | 1.1326 | -1.2128 | 12 | 0.9383 | 0.2072 | 0.4668 | 0.2789 | 0.4214 | 0.6447 | 0.383 | 0.5674 | -0.6405 | 1.3186 | 0.3067 | -0.2766 | 0.7712 | 0.5031 | 0.0156 | 1.4496 | -0.053 | -0.2468 | 0.7101 | 0.0843 | 0.9026 | -21.8806 | 6.8122 | 1.433 | 13 | 0.3263 | 0.1153 | 0.1431 | 0.5979 | 0.5958 | 0.5009 | 0.1127 | 0.0754 | -0.0502 | 0.3342 | 0.035 | -0.1122 | 0.0772 | 0.0589 | -0.0001 | 1.0056 | -0.1036 | -0.1107 | 0.7679 | 0.0137 | 0.8118 | -22.793 | 14.5154 | -0.4441 | 14 | 0.5141 | 0.3791 | -0.2573 | 0.5663 | 0.0259 | 0.221 | 0.7555 | 0.1002 | -0.2644 | 0.4459 | 0.061 | 0.0587 | 0.8431 | 0.4163 | 0.0007 | 1.2025 | 0.0068 | -0.2399 | 0.7306 | -0.07 | 1.027 | -17.2096 | 16.9044 | 3.5426 | 15 | 0.0714 | 0.0006 | -0.0571 | 0.2543 | 0.2051 | 0.172 | -0.1141 | -0.1829 | 0.2394 | 0.8752 | 0.4948 | 0.1148 | 1.3664 | -0.1734 | 0.0025 | 1.2797 | -0.0169 | -0.0901 | 0.8317 | 0.0724 | 1.0083 | -19.218 | 19.2376 | 12.5017 | 16 | 0.3689 | 0.3898 | 0.1655 | 0.3712 | 0.1902 | 0.1023 | 0.4167 | 0.0445 | 0.2564 | -0.4032 | -0.0971 | -0.0481 | 1.2475 | -0.6472 | 0.0003 | 0.8937 | 0.013 | 0.0002 | 0.655 | -0.0394 | 0.8309 | -14.3486 | 23.7025 | 8.6187 | 17 | 0.1471 | -0.215 | 0.0116 | 0.3119 | -0.0141 | 0.4672 | 0.0555 | 0.1908 | -0.3786 | -0.2783 | 0.1135 | -0.1031 | 1.1517 | 0.6745 | -0 | 0.9905 | 0.0796 | -0.008 | 0.6015 | -0.0475 | 0.7432 | -9.965 | 31.8069 | 12.8174 |
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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 21 through 32 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 33 through 92 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 93 through 112 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 113 through 137 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 138 through 157 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 158 through 177 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 178 through 187 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 188 through 211 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 212 through 241 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 40 through 59 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 60 through 99 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 100 through 119 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 120 through 147 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 148 through 177 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 178 through 187 )16 | X-RAY DIFFRACTION | 16 | chain 'B' | | | | | | | | | | | | | | | |
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