Software | Name | Version | Classification |
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PHENIX | 1.16_3549refinementSCALEPACK | | data scalingPDB_EXTRACT | 3.25 | data extractionHKL-3000 | | data reductionHKL-3000 | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3sj7 Resolution: 2.198→49.918 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.03
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2361 | 2292 | 4.9 % |
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Rwork | 0.1763 | - | - |
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obs | 0.1792 | 46778 | 89.89 % |
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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: 121.59 Å2 / Biso mean: 36.6782 Å2 / Biso min: 5.57 Å2 |
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Refinement step | Cycle: final / Resolution: 2.198→49.918 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 7345 | 0 | 13 | 378 | 7736 |
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Biso mean | - | - | 62.28 | 37.82 | - |
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Num. residues | - | - | - | - | 988 |
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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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2.1985-2.2463 | 0.2925 | 53 | 0.2537 | 1085 | 36 | 2.2463-2.2985 | 0.3169 | 62 | 0.2547 | 1514 | 48 | 2.2985-2.356 | 0.3006 | 117 | 0.2425 | 2182 | 70 | 2.356-2.4197 | 0.3343 | 161 | 0.251 | 2727 | 90 | 2.4197-2.4909 | 0.3522 | 137 | 0.2407 | 3068 | 99 | 2.4909-2.5713 | 0.2997 | 162 | 0.2237 | 3085 | 100 | 2.5713-2.6632 | 0.2736 | 171 | 0.2103 | 3075 | 100 | 2.6632-2.7698 | 0.2649 | 160 | 0.2095 | 3049 | 100 | 2.7698-2.8959 | 0.2779 | 162 | 0.2034 | 3059 | 100 | 2.8959-3.0485 | 0.272 | 162 | 0.2037 | 3076 | 99 | 3.0485-3.2395 | 0.2378 | 142 | 0.1955 | 3071 | 100 | 3.2395-3.4896 | 0.2658 | 154 | 0.1809 | 3094 | 100 | 3.4896-3.8406 | 0.2108 | 173 | 0.1551 | 3077 | 99 | 3.8406-4.3961 | 0.1723 | 167 | 0.1341 | 3070 | 99 | 4.3961-5.5374 | 0.1788 | 153 | 0.1252 | 3119 | 100 | 5.5374-49.918 | 0.1867 | 156 | 0.1426 | 3135 | 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 | 0.015 | 0.0049 | 0.0093 | 0.0026 | -0.0006 | 0.0308 | 0.0186 | 0.0078 | -0.0044 | -0.027 | 0.0109 | 0.0083 | 0.0153 | -0.0168 | 0.0391 | 0.2914 | -0.1359 | -0.0878 | 0.1931 | 0.0784 | 0.1235 | 32.1478 | 40.4052 | 31.871 | 2 | 0.0003 | -0.0003 | -0.001 | -0.0001 | 0.0018 | 0.0038 | 0.059 | 0.0553 | 0.0024 | -0.0233 | 0.0114 | 0.0104 | 0.0331 | -0.0001 | 0 | 0.4832 | -0.0553 | -0.1308 | 0.2726 | 0.0814 | 0.2046 | 30.5098 | 37.4917 | 24.8189 | 3 | 0.0014 | -0.0007 | -0.0014 | 0.0014 | 0.0013 | 0.0057 | -0.0016 | 0.0407 | 0.0262 | -0.0249 | 0.0274 | 0.0222 | 0.024 | 0.0058 | 0 | 0.6345 | 0.0744 | -0.0194 | 0.4241 | -0.031 | 0.2891 | 41.581 | 32.5303 | 25.9316 | 4 | -0.0004 | 0.0005 | -0.0004 | 0.0003 | 0.0002 | 0.0008 | 0.0391 | 0.0259 | 0.0292 | -0.007 | -0.0196 | -0.0066 | 0.0003 | 0.0133 | 0.0183 | 0.3186 | -0.0885 | 0.0644 | 0.2218 | 0.0999 | 0.0405 | 43.3493 | 40.744 | 28.5985 | 5 | 0.1518 | 0.0069 | 0.0342 | 0.0001 | 0.001 | 0.0081 | 0.1029 | 0.1013 | -0.0263 | -0.0389 | 0.0284 | -0.0339 | 0.0503 | 0.1022 | 0.0942 | 0.3197 | -0.0289 | 0.0236 | 0.1162 | -0.0385 | 0.0685 | 43.6908 | 24.1717 | 38.802 | 6 | 0.0555 | 0.0119 | 0.0148 | 0.007 | 0.0061 | 0.0065 | 0.0739 | 0.0274 | 0.0176 | -0.0537 | 0.0265 | 0.0272 | 0.0894 | 0.055 | 0.0971 | 0.2459 | -0.1237 | -0.0152 | 0.0694 | 0.0158 | 0.144 | 40.8801 | 32.7344 | 45.9837 | 7 | 0.0107 | 0.0045 | 0.0012 | 0.0022 | 0.0015 | 0.0007 | 0.0128 | 0.0086 | -0.0154 | -0.0019 | -0.0093 | 0.0135 | 0.0045 | -0.0114 | 0.0082 | 0.2296 | -0.2239 | -0.1366 | 0.2028 | -0 | 0.2743 | 18.1251 | 27.1525 | 44.3504 | 8 | 0.0121 | 0.005 | -0.0007 | 0.0066 | -0.0069 | 0.0077 | 0.016 | 0 | 0.0362 | -0.0264 | 0.0129 | -0.014 | -0.0131 | -0.0186 | 0.0108 | 0.1885 | -0.1518 | -0.0646 | 0.1617 | 0.0349 | 0.1845 | 32.7635 | 43.246 | 44.5688 | 9 | 0.004 | 0.0058 | -0.0024 | 0.0106 | -0.003 | 0.0089 | -0.0098 | -0.0006 | -0.0029 | -0.0147 | 0.0183 | -0.0015 | -0.0063 | 0.0011 | 0.0017 | 0.2121 | -0.19 | -0.0759 | 0.1396 | 0.0602 | 0.2899 | 24.9205 | 27.4881 | 56.4571 | 10 | 0.0083 | -0.0037 | -0.001 | 0.0092 | -0.023 | 0.0735 | 0.0122 | -0.0233 | 0.071 | -0.0203 | 0.0703 | -0.017 | -0.0481 | -0.0123 | 0.037 | 0.1858 | -0.0523 | -0.0291 | 0.1458 | -0.0517 | 0.3351 | 20.6455 | 59.6759 | 56.5864 | 11 | 0.0813 | 0.0834 | -0.0252 | 0.1466 | -0.1053 | 0.125 | 0.0056 | -0.0461 | 0.1122 | 0.1391 | 0.1121 | 0.0648 | -0.0476 | 0.0057 | 0.114 | 0.2054 | 0.0881 | -0.0187 | 0.2028 | -0.1044 | 0.1718 | 23.1195 | 51.6225 | 70.4126 | 12 | 0.0321 | -0.084 | -0.0339 | 0.2032 | -0.0184 | 0.2187 | -0.0026 | -0.0146 | 0.1002 | -0.0502 | 0.1716 | 0.037 | -0.1383 | -0.0211 | 0.4504 | -0.3562 | -0.4377 | -0.0317 | -0.1926 | -0.0114 | 0.101 | 30.7157 | 44.7295 | 59.0979 | 13 | 0.0005 | -0.0003 | 0 | 0.003 | 0.0029 | 0.003 | -0.0091 | -0.0114 | -0.0119 | 0.0129 | 0.0105 | 0.0068 | 0.0169 | 0.0096 | 0.0033 | 0.196 | 0.0168 | 0.0581 | 0.3466 | 0.1851 | 0.1548 | 39.954 | 18.8999 | 87.6775 | 14 | 0.0102 | -0.0024 | 0.0095 | 0.0004 | -0.0021 | 0.0145 | 0.0227 | -0.0362 | -0.0276 | 0.044 | -0.0324 | 0.0117 | 0.0365 | -0.0259 | -0.0135 | 0.3242 | 0.1231 | 0.052 | 0.5676 | 0.1693 | 0.2002 | 36.2258 | 21.1736 | 94.3319 | 15 | 0.0235 | 0.0177 | -0.0296 | 0.0751 | -0.0158 | 0.0452 | 0.0219 | -0.0321 | 0.0406 | 0.0921 | 0.075 | 0.103 | -0.0353 | 0.0267 | 0.081 | 0.1772 | 0.0332 | 0.07 | 0.3946 | 0.1299 | 0.0605 | 32.4368 | 31.1515 | 86.1509 | 16 | 0.0125 | 0.0058 | 0.0076 | 0.0391 | 0.0095 | 0.0122 | 0.0082 | -0.0193 | 0.0201 | 0.0712 | 0.0732 | 0.0018 | -0.0103 | 0.0341 | 0.0555 | 0.2019 | 0.0842 | 0.0389 | 0.4743 | 0.0056 | 0.0819 | 33.8131 | 37.3522 | 83.8812 | 17 | 0.0275 | -0.0042 | -0.0097 | 0.0246 | -0.0026 | 0.0216 | -0.0021 | -0.0237 | 0.0041 | -0.0057 | 0.04 | 0.0584 | 0.0083 | 0.0166 | 0.0263 | 0.0788 | -0.0811 | 0.0167 | 0.2278 | 0.0717 | 0.0996 | 34.8716 | 28.2505 | 74.0644 | 18 | 0.0503 | -0.0074 | -0.0052 | 0.0404 | 0.0007 | 0.0385 | 0.0007 | -0.0747 | 0.0022 | 0.038 | 0.0733 | 0.0199 | -0.0132 | -0.0108 | 0.0927 | 0.0904 | -0.054 | 0.0253 | 0.2004 | 0.0351 | 0.0667 | 37.0211 | 28.7921 | 75.8481 | 19 | 0.0045 | -0.0024 | -0.0023 | 0.003 | -0.003 | 0.0351 | -0.0172 | -0.0606 | -0.0597 | -0.0066 | 0.0388 | 0.0417 | 0.0679 | 0.0318 | 0.0089 | 0.1141 | -0.0449 | 0.0157 | 0.1966 | 0.1376 | 0.1807 | 38.8475 | 16.7397 | 73.0372 | 20 | 0.001 | 0.0004 | -0.0035 | 0.0045 | 0.0017 | 0.0097 | -0.0159 | -0.0088 | -0.0201 | -0.0091 | -0.0184 | 0.0223 | 0.0031 | 0.0031 | -0.0144 | 0.1755 | -0.1158 | -0.0377 | 0.1007 | 0.0583 | 0.2444 | 30.7218 | 18.96 | 61.2149 | 21 | 0.0208 | 0.0012 | 0.0022 | 0.0226 | 0.0052 | 0.0274 | 0.033 | -0.0346 | -0.1327 | 0.039 | 0.0348 | -0.0409 | 0.0923 | 0.0521 | 0.0415 | 0.4384 | 0.2142 | 0.0071 | 0.2757 | 0.1154 | 0.3018 | 58.6216 | 5.0546 | 60.1595 | 22 | 0.1163 | -0.042 | 0.0283 | 0.0994 | -0.0383 | 0.2292 | 0.0929 | -0.0367 | -0.1019 | -0.0995 | -0.0077 | -0.1174 | 0.1863 | 0.2435 | 0.1717 | 0.0926 | -0.0156 | 0.0311 | 0.0664 | 0.0382 | 0.1102 | 49.7403 | 20.9772 | 58.6035 |
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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 1 through 24 )A1 - 24 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 25 through 50 )A25 - 50 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 51 through 69 )A51 - 69 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 70 through 86 )A70 - 86 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 87 through 129 )A87 - 129 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 130 through 183 )A130 - 183 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 184 through 213 )A184 - 213 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 214 through 235 )A214 - 235 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 236 through 252 )A236 - 252 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid -1 through 50 ) | B-1 - 50 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 51 through 112 )B51 - 112 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 113 through 252 )B113 - 252 | 13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 2 through 24 )C2 - 24 | 14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 25 through | | | | | | | | | | | | | | | | | | | | | | | | | |
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