Software | Name | Version | Classification |
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SCALA | | data scalingPHENIX | dev_2356refinementPDB_EXTRACT | 3.2 | data extractionXDS | | data reductionMoRDa | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3awd Resolution: 1.45→41.934 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.1
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2363 | 2095 | 1.36 % |
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Rwork | 0.2062 | - | - |
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obs | 0.2066 | 153836 | 98.37 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 62.71 Å2 / Biso mean: 18.4934 Å2 / Biso min: 3.14 Å2 |
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Refinement step | Cycle: final / Resolution: 1.45→41.934 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 7292 | 0 | 176 | 1037 | 8505 |
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Biso mean | - | - | 20.91 | 29.09 | - |
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Num. residues | - | - | - | - | 1032 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 7706 | X-RAY DIFFRACTION | f_angle_d0.959 | 10571 | X-RAY DIFFRACTION | f_chiral_restr0.081 | 1264 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1375 | X-RAY DIFFRACTION | f_dihedral_angle_d16.745 | 2693 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.45-1.4838 | 0.3859 | 109 | 0.315 | 9557 | 9666 | 93 | 1.4838-1.5209 | 0.2771 | 132 | 0.2502 | 10258 | 10390 | 100 | 1.5209-1.562 | 0.2239 | 149 | 0.2226 | 10169 | 10318 | 100 | 1.562-1.608 | 0.2387 | 143 | 0.208 | 10237 | 10380 | 100 | 1.608-1.6599 | 0.2673 | 141 | 0.2065 | 10235 | 10376 | 100 | 1.6599-1.7192 | 0.2496 | 162 | 0.2045 | 10218 | 10380 | 100 | 1.7192-1.788 | 0.2383 | 130 | 0.2082 | 10214 | 10344 | 100 | 1.788-1.8694 | 0.2876 | 133 | 0.22 | 10216 | 10349 | 99 | 1.8694-1.968 | 0.2945 | 130 | 0.2602 | 9640 | 9770 | 94 | 1.968-2.0913 | 0.2443 | 148 | 0.208 | 10209 | 10357 | 99 | 2.0913-2.2527 | 0.2226 | 125 | 0.2157 | 9968 | 10093 | 97 | 2.2527-2.4794 | 0.2495 | 132 | 0.2031 | 10027 | 10159 | 97 | 2.4794-2.8381 | 0.2263 | 148 | 0.1956 | 10256 | 10404 | 100 | 2.8381-3.5754 | 0.2044 | 159 | 0.1824 | 10251 | 10410 | 99 | 3.5754-41.9516 | 0.2145 | 154 | 0.1835 | 10286 | 10440 | 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 | 3.1138 | -0.8445 | 0.8178 | 3.8825 | -3.19 | 5.9865 | -0.0538 | 0.1992 | -0.1452 | -0.2571 | -0.0208 | -0.053 | 0.2387 | 0.1496 | 0.0647 | 0.1043 | -0.0484 | -0.002 | 0.046 | -0.0068 | 0.0965 | -47.3097 | -10.4741 | 13.3799 | 2 | 3.4701 | 0.6436 | 0.2807 | 2.6335 | 1.3176 | 2.0084 | 0.0061 | 0.1863 | -0.256 | -0.3457 | 0.034 | 0.4264 | 0.0642 | -0.148 | -0.0629 | 0.1679 | -0.0512 | -0.0077 | 0.1132 | 0.024 | 0.1426 | -57.739 | -8.3234 | 11.152 | 3 | 0.7952 | 0.0182 | 0.0208 | 3.4178 | -1.7686 | 1.7007 | -0.0433 | 0.0595 | 0.0345 | -0.1645 | 0.0721 | 0.1605 | 0.0943 | -0.1166 | -0.0484 | 0.1233 | -0.022 | -0.0186 | 0.0873 | 0.0012 | 0.0768 | -56.7847 | 2.5742 | 13.9616 | 4 | 1.0494 | 0.0898 | -0.1335 | 1.6098 | -0.6091 | 0.6818 | -0.0278 | -0.019 | -0.0388 | 0.028 | 0.0476 | 0.1389 | -0.0014 | -0.0677 | -0.0287 | 0.0984 | -0.0133 | 0.0047 | 0.0699 | -0.001 | 0.0767 | -51.4126 | 7.6426 | 15.9651 | 5 | 1.2675 | -0.401 | 1.1665 | 1.5191 | -1.2699 | 3.8041 | -0.0127 | -0.0438 | -0.05 | 0.0235 | 0.0715 | 0.0664 | -0.0406 | 0.0449 | -0.0626 | 0.0988 | 0.0148 | 0.0295 | 0.0416 | 0.006 | 0.0841 | -46.3165 | 9.2359 | 21.5605 | 6 | 1.5408 | -0.1114 | -0.0358 | 1.5177 | 0.136 | 2.3868 | -0.0031 | 0.4339 | 0.0409 | -0.4363 | 0.3067 | 0.3014 | 0.1425 | -0.5026 | -0.1686 | 0.2304 | -0.0728 | -0.0377 | 0.2132 | 0.0385 | 0.1198 | -44.4053 | 2.1921 | 7.0654 | 7 | 0.7689 | 0.3787 | -0.534 | 1.1609 | -0.6196 | 1.7175 | -0.1124 | 0.2921 | -0.0337 | -0.4534 | 0.1789 | 0.0552 | 0.209 | -0.2101 | -0.0831 | 0.198 | -0.0445 | -0.0012 | 0.1598 | -0.0061 | 0.0914 | -38.222 | 0.7375 | 1.6208 | 8 | 1.5015 | -0.3766 | -0.3172 | 1.4702 | 0.4606 | 2.6262 | -0.001 | -0.0753 | -0.0427 | 0.0856 | 0.1405 | -0.0192 | -0.1449 | 0.0907 | -0.1258 | 0.0563 | -0.0061 | 0.0041 | 0.044 | -0.0159 | 0.0632 | -36.2942 | 0.3496 | 17.6683 | 9 | 3.8306 | 0.0284 | -0.4584 | 1.3152 | -0.5401 | 2.2404 | -0.1395 | 0.2926 | -0.1032 | -0.294 | 0.1597 | -0.0629 | 0.2716 | -0.1011 | -0.046 | 0.1494 | -0.0001 | 0.0316 | 0.0902 | -0.0232 | 0.0907 | -26.5686 | 12.3112 | -1.7662 | 10 | 3.5194 | 0.3845 | 0.7632 | 2.2776 | 1.4596 | 2.7331 | -0.0079 | -0.0547 | -0.2125 | 0.1032 | 0.0189 | -0.0307 | 0.1777 | 0.0413 | -0.0267 | 0.1258 | 0.0457 | 0.0258 | 0.0552 | 0.0036 | 0.135 | -20.3541 | -10.1659 | 18.7942 | 11 | 2.804 | -0.316 | 0.2824 | 1.6007 | -0.0108 | 1.2375 | -0.0358 | -0.2112 | -0.3989 | 0.2568 | 0.0838 | -0.3197 | 0.1404 | 0.1742 | -0.0811 | 0.1732 | 0.0738 | 0.0089 | 0.1397 | -0.0144 | 0.239 | -9.9806 | -8.8969 | 20.7518 | 12 | 0.6449 | -0.1376 | -0.0742 | 1.7296 | 0.1468 | 0.4156 | -0.0175 | -0.0016 | -0.0457 | 0.0548 | 0.0905 | -0.3226 | 0.0945 | 0.1158 | -0.0816 | 0.1034 | 0.0173 | 0.0078 | 0.1057 | -0.0275 | 0.1721 | -10.9868 | 4.8442 | 16.6287 | 13 | 0.7322 | -0.1417 | -0.3682 | 1.1163 | 0.2406 | 1.4565 | -0.0494 | -0.0342 | -0.0194 | 0.0398 | 0.0543 | -0.1546 | 0.1072 | 0.1011 | -0.0241 | 0.0928 | 0.0126 | 0.0113 | 0.0662 | -0.0167 | 0.0968 | -21.9895 | 6.4474 | 18.5898 | 14 | 0.9115 | -0.1983 | -0.4 | 1.4667 | 0.458 | 1.7874 | -0.0516 | -0.129 | -0.0514 | 0.2105 | 0.0196 | -0.0321 | 0.0715 | 0.0632 | 0.0267 | 0.1055 | 0.0048 | 0.0025 | 0.0767 | 0.0106 | 0.0749 | -32.1813 | 4.0343 | 27.7084 | 15 | 3.9825 | -1.0129 | -0.498 | 4.4838 | 2.7156 | 4.146 | 0.0263 | 0.1483 | 0.211 | -0.2604 | -0.027 | -0.0979 | -0.2912 | 0.0579 | -0.0226 | 0.1329 | -0.0474 | 0.0071 | 0.0549 | -0.0032 | 0.1282 | -20.1109 | 42.8493 | 15.3285 | 16 | 4.2421 | 0.5447 | 0.1679 | 2.3973 | -0.6297 | 1.5916 | -0.1732 | 0.2207 | 0.3593 | -0.2731 | 0.1135 | -0.4418 | -0.1634 | 0.2324 | 0.0075 | 0.1734 | -0.0756 | 0.018 | 0.1478 | -0.0547 | 0.2274 | -9.4896 | 41.5503 | 14.8206 | 17 | 0.4821 | -0.0111 | 0.0596 | 1.1118 | 0.1072 | 0.4537 | -0.0232 | 0.009 | 0.0413 | -0.0291 | 0.0712 | -0.2633 | -0.0861 | 0.1022 | -0.0532 | 0.1132 | -0.0068 | 0.0165 | 0.0927 | -0.0274 | 0.133 | -16.3714 | 26.9686 | 17.0003 | 18 | 2.6274 | 0.568 | 0.2953 | 2.3382 | 0.523 | 2.6585 | 0.0153 | 0.2688 | 0.0281 | -0.2607 | -0.0346 | -0.3291 | -0.062 | 0.2414 | 0.0046 | 0.204 | -0.0205 | 0.0441 | 0.1692 | 0.0157 | 0.1046 | -25.9699 | 27.6935 | -4.4622 | 19 | 0.9139 | 0.4169 | 0.5341 | 1.7632 | 1.1453 | 1.8402 | -0.0638 | 0.0491 | 0.0541 | -0.1347 | 0.0462 | -0.0033 | -0.0556 | 0.016 | 0.0367 | 0.0749 | 0.0056 | 0.015 | 0.0568 | 0.0091 | 0.0713 | -32.5397 | 29.6912 | 9.6901 | 20 | 3.8822 | 0.8839 | -0.7534 | 2.9545 | -1.5215 | 4.9958 | -0.0286 | -0.2197 | 0.2401 | 0.2297 | 0.0444 | 0.1096 | -0.2861 | 0.1211 | -0.0388 | 0.0962 | 0.0374 | 0.0255 | 0.0514 | 0.0027 | 0.1143 | -47.5589 | 43.1737 | 17.0674 | 21 | 3.1428 | -0.1293 | 0.0936 | 1.6271 | 1.0928 | 1.8285 | -0.0501 | -0.2201 | 0.3228 | 0.2341 | 0.1157 | 0.5161 | -0.0877 | -0.1673 | -0.0461 | 0.1305 | 0.0558 | 0.0431 | 0.1248 | 0.0372 | 0.1991 | -58.1764 | 41.2275 | 18.1343 | 22 | 0.9286 | 0.0745 | -0.102 | 3.2853 | -1.1381 | 0.7795 | -0.0085 | -0.0165 | -0.0039 | 0.1058 | 0.1351 | 0.291 | -0.0172 | -0.1179 | -0.1479 | 0.1073 | 0.0085 | 0.0262 | 0.1022 | 0.0171 | 0.1043 | -56.7943 | 30.1257 | 15.245 | 23 | 3.8341 | 1.3253 | -0.6392 | 7.5346 | -2.3253 | 1.9923 | -0.0454 | -0.1524 | -0.0427 | 0.223 | 0.1932 | 0.4279 | -0.0114 | -0.173 | -0.1119 | 0.1224 | 0.0256 | 0.0247 | 0.1083 | 0.0215 | 0.1505 | -58.3625 | 18.7099 | 20.3497 | 24 | 3.0588 | 1.1806 | -1.1056 | 3.4212 | -1.2059 | 2.1516 | -0.0078 | 0.2135 | 0.0997 | -0.2236 | 0.0494 | 0.1281 | -0.1134 | -0.0755 | -0.0903 | 0.128 | 0.0103 | -0.0152 | 0.1086 | 0.0309 | 0.1202 | -53.2582 | 30.6684 | 4.7613 | 25 | 0.9696 | 0.1172 | -0.3135 | 1.6147 | -0.6184 | 1.4071 | -0.0143 | 0.0168 | 0.0154 | -0.0171 | 0.0522 | 0.0913 | -0.0009 | -0.0666 | -0.0403 | 0.0645 | 0.0031 | 0.0047 | 0.0481 | 0.0005 | 0.0605 | -45.2511 | 23.9772 | 13.2117 | 26 | 1.4623 | 0.0267 | -0.5046 | 1.3403 | 0.3148 | 2.4723 | -0.0302 | -0.3427 | -0.01 | 0.3905 | 0.3305 | 0.3809 | -0.2182 | -0.6122 | -0.124 | 0.1961 | 0.1074 | 0.0767 | 0.2457 | 0.0587 | 0.1394 | -45.8278 | 30.3939 | 24.251 | 27 | 3.1558 | -1.8471 | 0.7652 | 2.086 | 0.4303 | 2.7423 | -0.0679 | -0.4196 | -0.1474 | 0.4565 | 0.1053 | 0.3014 | 0.0295 | -0.4073 | -0.0678 | 0.2536 | 0.0354 | 0.0438 | 0.2226 | 0.0034 | 0.1189 | -40.9504 | 27.7266 | 36.7844 | 28 | 0.8804 | 0.0346 | 0.1991 | 1.0947 | -0.9032 | 3.5688 | -0.0153 | -0.0391 | 0.0897 | 0.107 | 0.0524 | 0.0265 | -0.0814 | -0.044 | -0.0516 | 0.0686 | 0.011 | 0.0109 | 0.0581 | -0.0064 | 0.0809 | -37.7869 | 34.5037 | 16.76 | 29 | 4.8873 | -0.2439 | 1.6057 | 1.0685 | -1.6975 | 3.1812 | -0.1092 | -0.2473 | -0.0118 | 0.1472 | 0.0568 | -0.0279 | -0.1872 | -0.0663 | 0.0283 | 0.1756 | 0.0183 | 0.0062 | 0.1022 | -0.0143 | 0.0997 | -29.0724 | 20.3835 | 34.865 |
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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 3 through 31 )A3 - 31 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 32 through 64 )A32 - 64 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 65 through 102 )A65 - 102 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 103 through 152 )A103 - 152 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 153 through 174 )A153 - 174 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 175 through 195 )A175 - 195 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 196 through 228 )A196 - 228 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 229 through 245 )A229 - 245 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 246 through 261 )A246 - 261 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 3 through 31 )B3 - 31 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 32 through 64 )B32 - 64 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 65 through 131 )B65 - 131 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 132 through 196 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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