Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementPDB_EXTRACT | 3.22 | data extractionXDS | | data scaling Coot | | model buildingPHASER | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3v34 Resolution: 1.94→44.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.67 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2133 | 1774 | 5 % |
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Rwork | 0.1723 | 33688 | - |
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obs | 0.1744 | 35462 | 99.86 % |
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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: 122.35 Å2 / Biso mean: 42.8204 Å2 / Biso min: 19.24 Å2 |
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Refinement step | Cycle: final / Resolution: 1.94→44.5 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2712 | 0 | 33 | 260 | 3005 |
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Biso mean | - | - | 45.63 | 48.99 | - |
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Num. residues | - | - | - | - | 334 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.015 | 2803 | X-RAY DIFFRACTION | f_angle_d1.399 | 3769 | X-RAY DIFFRACTION | f_chiral_restr0.074 | 401 | X-RAY DIFFRACTION | f_plane_restr0.008 | 493 | X-RAY DIFFRACTION | f_dihedral_angle_d11.777 | 1073 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Number | Refine-ID | Rms | Type |
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1 | 1 | A1568 | X-RAY DIFFRACTION | 7.207 | TORSIONAL1 | 2 | B1568 | X-RAY DIFFRACTION | 7.207 | TORSIONAL | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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1.94-1.9922 | 0.2932 | 134 | 0.2626 | 2534 | 99 | 1.9922-2.0508 | 0.2443 | 134 | 0.235 | 2551 | 100 | 2.0508-2.117 | 0.2789 | 133 | 0.2144 | 2522 | 100 | 2.117-2.1926 | 0.2416 | 134 | 0.1906 | 2554 | 100 | 2.1926-2.2804 | 0.208 | 135 | 0.1858 | 2556 | 100 | 2.2804-2.3842 | 0.2406 | 134 | 0.1804 | 2549 | 100 | 2.3842-2.5099 | 0.2415 | 135 | 0.1783 | 2575 | 100 | 2.5099-2.6671 | 0.2063 | 135 | 0.1902 | 2570 | 100 | 2.6671-2.873 | 0.237 | 137 | 0.1855 | 2594 | 100 | 2.873-3.1621 | 0.2288 | 137 | 0.1826 | 2604 | 100 | 3.1621-3.6195 | 0.2072 | 137 | 0.1726 | 2603 | 100 | 3.6195-4.5594 | 0.1959 | 140 | 0.138 | 2669 | 100 | 4.5594-44.5 | 0.1802 | 149 | 0.1563 | 2807 | 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 | 5.2846 | -4.5163 | -0.6992 | 8.1715 | -3.8051 | 4.6566 | -0.0469 | 0.0132 | -0.1105 | 0.0012 | 0.0796 | 0.1865 | -0.1415 | -0.1171 | -0.074 | 0.2416 | -0.1064 | 0.0067 | 0.1346 | -0.0401 | 0.1875 | -4.371 | 35.3403 | 3.5126 | 2 | 3.1232 | 0.1673 | 0.1125 | 5.2768 | -4.9601 | 7.3868 | -0.0471 | -0.1846 | 0.1397 | 0.4646 | 0.0951 | -0.0366 | -0.6691 | 0.0773 | -0.0302 | 0.2639 | -0.0583 | -0.0014 | 0.1573 | -0.0629 | 0.1591 | -3.6044 | 39.2561 | 7.234 | 3 | 8.2956 | 1.9367 | 5.3367 | 7.4716 | 2.5892 | 4.2344 | -0.1857 | 0.4679 | 0.9981 | -0.432 | -0.1048 | 0.1447 | -0.9363 | 0.0474 | 0.3401 | 0.2727 | 0.0021 | 0.0394 | 0.2646 | 0.0226 | 0.3313 | -8.0213 | 49.1766 | -1.0945 | 4 | 3.886 | 1.9321 | -2.8487 | 5.2567 | -3.9433 | 6.3748 | 0.1046 | 0.2043 | 0.2039 | -0.2396 | 0.2582 | 0.1519 | -0.0899 | 0.2549 | -0.3855 | 0.2524 | -0.0956 | -0.0438 | 0.2246 | -0.0119 | 0.2657 | 3.4744 | 46.7329 | -7.0565 | 5 | 7.0987 | -5.2508 | 4.6146 | 4.7417 | -5.7239 | 9.5632 | 0.2177 | 0.5928 | -0.0534 | -0.6125 | -0.3015 | -0.6816 | 0.2517 | 0.709 | 0.1247 | 0.2834 | -0.0696 | 0.0469 | 0.339 | -0.0385 | 0.3635 | 8.9559 | 34.1216 | -1.2893 | 6 | 8.0972 | -1.2879 | -1.6427 | 5.339 | 0.9261 | 3.3651 | -0.0469 | 0.4409 | -0.3974 | -0.3039 | 0.1089 | -0.4208 | 0.2004 | 0.0603 | -0.0297 | 0.2679 | -0.0779 | 0.0082 | 0.1796 | -0.0242 | 0.2518 | 0.7561 | 27.0884 | -0.0063 | 7 | 5.0408 | 1.778 | -2.9197 | 7.136 | -0.8445 | 3.6657 | 0.3705 | -0.7041 | -0.9402 | 0.4849 | -0.1933 | -0.3456 | 0.8199 | 0.0876 | -0.1983 | 0.4292 | -0.0339 | -0.0844 | 0.3076 | 0.0967 | 0.4365 | -0.2062 | 19.7986 | 12.4236 | 8 | 5.1101 | 2.7053 | -1.3451 | 5.649 | -0.67 | 7.6477 | 0.0791 | -0.1646 | -0.2914 | 0.4111 | -0.3625 | -0.2994 | -0.0595 | -0.0565 | 0.2653 | 0.2729 | -0.1613 | -0.0424 | 0.2918 | 0.012 | 0.3219 | 17.3843 | 53.2972 | 0.109 | 9 | 3.2271 | 1.4209 | -0.1081 | 7.1147 | 1.2612 | 3.0291 | 0.3745 | -0.3158 | -0.4376 | 0.6014 | -0.2899 | -1.0894 | 0.1184 | 0.2876 | -0.0889 | 0.2894 | -0.1504 | -0.092 | 0.3653 | 0.0667 | 0.4504 | 23.0052 | 52.8389 | 1.8619 | 10 | 7.2552 | 1.1847 | -0.9797 | 3.8462 | -1.6922 | 3.2712 | 0.875 | -1.3844 | 0.6042 | 1.4079 | -0.631 | -0.3337 | -0.8858 | 0.2889 | -0.3865 | 0.786 | -0.4369 | -0.0033 | 0.6764 | -0.0143 | 0.4497 | 19.9303 | 61.5653 | 12.0269 | 11 | 9.4833 | -3.1985 | -0.3937 | 6.4046 | 0.4959 | 4.3382 | 0.591 | -0.3238 | 0.4733 | 0.494 | -0.4115 | 0.2879 | -0.2258 | -0.5769 | -0.1798 | 0.3192 | -0.2026 | 0.0772 | 0.4326 | -0.0189 | 0.4267 | 19.9163 | 70.5416 | 2.4545 | 12 | 3.2232 | 0.3342 | 1.6957 | 4.5514 | 4.3962 | 4.8754 | -0.2588 | 0.4306 | 0.256 | -0.2125 | -0.2652 | -0.0454 | -0.5276 | -0.1265 | 0.4544 | 0.3635 | -0.1446 | 0.0125 | 0.3656 | 0.0356 | 0.3188 | 20.5121 | 62.6724 | -10.3745 | 13 | 4.6946 | 1.4181 | 0.938 | 4.0026 | -0.7101 | 3.2413 | -0.181 | 0.2926 | 0.1937 | -0.3393 | 0.132 | -0.1179 | -0.1942 | 0.0737 | 0.0699 | 0.298 | -0.1465 | 0.0276 | 0.2944 | -0.0421 | 0.2639 | 14.091 | 54.0024 | -9.5388 | 14 | 3.703 | -1.1091 | 3.4163 | 5.3826 | -1.8419 | 6.4324 | 0.0756 | 0.4152 | -0.8178 | -0.8928 | 0.2355 | -0.8016 | 0.4994 | 0.0838 | -0.199 | 0.4119 | -0.1061 | 0.126 | 0.3435 | -0.1595 | 0.4334 | 17.0026 | 41.5878 | -13.4781 |
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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 261 through 286 )A261 - 286 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 287 through 314 )A287 - 314 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 315 through 334 )A315 - 334 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 335 through 354 )A335 - 354 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 355 through 365 )A355 - 365 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 366 through 406 )A366 - 406 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 407 through 428 )A407 - 428 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 262 through 286 )B262 - 286 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 287 through 314 )B287 - 314 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 315 through 334 )B315 - 334 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 335 through 354 )B335 - 354 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 355 through 365 )B355 - 365 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 366 through 406 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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