Software | Name | Version | Classification |
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SCALEPACK | | data scalingPHENIX | 1.12_2829refinementPDB_EXTRACT | 3.24 | data extractionHKL-3000 | | data reductionHKL-3000 | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1cev.pdb Resolution: 1.91→48.444 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.62
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2034 | 6774 | 4.96 % |
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Rwork | 0.1611 | - | - |
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obs | 0.1631 | 136503 | 92.69 % |
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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: 107.59 Å2 / Biso mean: 23.163 Å2 / Biso min: 3.63 Å2 |
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Refinement step | Cycle: final / Resolution: 1.91→48.444 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 13058 | 0 | 17 | 1615 | 14690 |
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Biso mean | - | - | 20.85 | 33.67 | - |
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Num. residues | - | - | - | - | 1726 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 13300 | X-RAY DIFFRACTION | f_angle_d0.777 | 17981 | X-RAY DIFFRACTION | f_chiral_restr0.054 | 2073 | X-RAY DIFFRACTION | f_plane_restr0.005 | 2335 | X-RAY DIFFRACTION | f_dihedral_angle_d13.731 | 7980 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.9103-1.932 | 0.2628 | 96 | 0.2043 | 1923 | 2019 | 41 | 1.932-1.9547 | 0.2561 | 149 | 0.2056 | 2893 | 3042 | 63 | 1.9547-1.9786 | 0.2465 | 199 | 0.1983 | 3115 | 3314 | 68 | 1.9786-2.0036 | 0.2103 | 167 | 0.1956 | 3413 | 3580 | 74 | 2.0036-2.03 | 0.2518 | 195 | 0.1897 | 3645 | 3840 | 79 | 2.03-2.0578 | 0.2407 | 221 | 0.1831 | 3858 | 4079 | 84 | 2.0578-2.0872 | 0.2367 | 209 | 0.1878 | 4057 | 4266 | 88 | 2.0872-2.1184 | 0.2323 | 225 | 0.1839 | 4332 | 4557 | 93 | 2.1184-2.1515 | 0.2239 | 223 | 0.1743 | 4472 | 4695 | 96 | 2.1515-2.1867 | 0.2342 | 237 | 0.1722 | 4481 | 4718 | 97 | 2.1867-2.2244 | 0.2122 | 222 | 0.1736 | 4611 | 4833 | 100 | 2.2244-2.2649 | 0.2471 | 222 | 0.1692 | 4653 | 4875 | 100 | 2.2649-2.3084 | 0.223 | 233 | 0.166 | 4625 | 4858 | 100 | 2.3084-2.3556 | 0.2282 | 214 | 0.1648 | 4638 | 4852 | 100 | 2.3556-2.4068 | 0.21 | 267 | 0.1614 | 4616 | 4883 | 100 | 2.4068-2.4628 | 0.2175 | 239 | 0.1634 | 4661 | 4900 | 100 | 2.4628-2.5244 | 0.1977 | 255 | 0.1611 | 4624 | 4879 | 100 | 2.5244-2.5926 | 0.2036 | 239 | 0.1628 | 4603 | 4842 | 99 | 2.5926-2.6689 | 0.2354 | 248 | 0.1734 | 4601 | 4849 | 99 | 2.6689-2.755 | 0.2295 | 263 | 0.1657 | 4626 | 4889 | 100 | 2.755-2.8535 | 0.2181 | 246 | 0.1611 | 4661 | 4907 | 100 | 2.8535-2.9677 | 0.1979 | 233 | 0.1614 | 4702 | 4935 | 100 | 2.9677-3.1028 | 0.2147 | 247 | 0.1714 | 4640 | 4887 | 100 | 3.1028-3.2663 | 0.2059 | 234 | 0.1592 | 4693 | 4927 | 100 | 3.2663-3.4709 | 0.174 | 227 | 0.1536 | 4698 | 4925 | 99 | 3.4709-3.7388 | 0.1858 | 246 | 0.1479 | 4682 | 4928 | 100 | 3.7388-4.1149 | 0.1812 | 253 | 0.1364 | 4719 | 4972 | 100 | 4.1149-4.7099 | 0.1591 | 237 | 0.1264 | 4756 | 4993 | 100 | 4.7099-5.9322 | 0.166 | 265 | 0.1476 | 4773 | 5038 | 100 | 5.9322-48.4598 | 0.1999 | 263 | 0.1747 | 4958 | 5221 | 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 | 0.001 | -0.0006 | 0 | 0.0014 | -0.0008 | 0.0009 | 0.0047 | 0.0008 | 0.0223 | 0.0008 | 0.0139 | -0.0128 | 0.0004 | -0.0031 | -0 | 0.0926 | 0.031 | 0.0097 | 0.1079 | 0.0255 | 0.0851 | 175.5169 | 69.1242 | -34.5131 | 2 | 0.0029 | -0.0012 | -0.0021 | 0.0025 | 0.0007 | 0.002 | -0.0074 | 0.0085 | -0.003 | -0.0101 | -0.0095 | -0.0094 | 0.0119 | -0.0028 | -0.0111 | 0.0644 | 0.0366 | 0.0075 | 0.1021 | 0.0049 | 0.0227 | 173.143 | 58.397 | -42.3287 | 3 | 0.0023 | -0.0025 | -0.0008 | 0.0051 | 0.0004 | 0.0035 | 0.0095 | 0.0125 | 0.0204 | -0.0046 | 0.005 | -0.0103 | -0.0073 | -0.0062 | 0.0239 | 0.0881 | 0.0293 | 0.002 | 0.0946 | 0.0814 | 0.1068 | 173.6303 | 78.3848 | -37.2258 | 4 | 0.0041 | -0.0016 | -0.0035 | 0.0051 | 0 | 0.0041 | 0.0032 | 0.0031 | 0.0071 | -0.0147 | 0.0042 | 0.0043 | 0.0058 | 0.004 | 0.0033 | 0.0593 | 0.0553 | 0.0125 | 0.1004 | 0.0814 | 0.0467 | 165.7039 | 71.7782 | -38.374 | 5 | 0.0045 | -0.0031 | -0.0006 | 0.002 | 0.0011 | 0.0013 | 0.0078 | -0.0006 | 0.0162 | 0.0107 | 0.0037 | 0.0035 | -0.0067 | -0.0106 | -0.0003 | 0.0933 | 0.0587 | 0.0166 | 0.1015 | 0.025 | 0.0731 | 162.4325 | 72.8897 | -25.9733 | 6 | 0.003 | -0.0059 | -0.0033 | 0.0102 | 0.0074 | 0.005 | 0.0087 | 0.0072 | 0.0365 | 0.0138 | 0.0181 | -0.0051 | -0.0069 | -0.0143 | 0.0195 | 0.072 | 0.0868 | 0.0083 | 0.0644 | 0.0298 | 0.0618 | 164.2109 | 77.7284 | -25.4221 | 7 | 0.007 | -0.0026 | -0.0013 | 0.0073 | -0.0095 | 0.0146 | -0.0193 | -0.0062 | -0.002 | 0.0317 | 0.0055 | 0.0142 | -0.0085 | -0.0313 | -0.0149 | 0.0736 | 0.0622 | 0.0515 | 0.105 | 0.0141 | 0.0709 | 156.9821 | 65.4561 | -21.5499 | 8 | 0.0014 | 0.0008 | 0.0002 | 0.0013 | 0.0015 | 0.0032 | 0.0023 | -0.0033 | -0.0016 | 0.0041 | -0.0001 | -0.0013 | -0.0001 | 0.003 | 0.0004 | 0.1011 | 0.0303 | 0.0007 | 0.063 | 0.0101 | 0.0221 | 172.8445 | 57.4005 | -20.497 | 9 | 0.0007 | -0.0007 | 0 | 0.0005 | 0.0001 | 0.0002 | -0.0036 | 0.0017 | -0.0034 | 0.0028 | -0.0013 | 0.0062 | 0.0031 | -0.0001 | -0.0001 | 0.0533 | 0.0016 | 0.0136 | 0.0835 | -0.0078 | 0.0443 | 159.3981 | 53.0849 | -30.0795 | 10 | 0.0019 | 0.0007 | 0.0013 | 0.0019 | -0.0003 | 0.0045 | 0.0012 | 0.0085 | -0.0042 | 0.0024 | -0.0072 | -0.003 | 0.0096 | -0.0056 | -0.0028 | 0.0744 | 0.0321 | 0.0053 | 0.0869 | 0.0192 | 0.026 | 169.4636 | 56.8015 | -33.2515 | 11 | 0.0042 | 0.0011 | 0.0122 | 0.0104 | 0.0011 | 0.0453 | -0.0379 | 0.0461 | -0.0842 | 0.0089 | -0.0288 | 0.046 | 0.0172 | -0.004 | -0.0528 | 0.0755 | -0.0699 | 0.0401 | 0.0157 | -0.145 | 0.2236 | 173.4371 | 18.8944 | -27.2142 | 12 | 0.0004 | -0.0003 | 0.0005 | 0.0005 | -0.0003 | 0.0012 | -0.0018 | 0.0099 | -0.0014 | -0.0012 | -0.0001 | 0.0075 | -0.0029 | 0.0031 | -0.0008 | 0.0915 | -0.0452 | -0.0183 | 0.1084 | -0.082 | 0.1532 | 161.5956 | 26.9267 | -34.2354 | 13 | 0.0659 | 0.0105 | 0.0025 | 0.0075 | 0.0019 | -0.0014 | -0.0219 | 0.0712 | -0.0958 | -0.0109 | -0.0327 | 0.14 | -0.0099 | -0.0672 | -0.0152 | -0.0312 | -0.118 | -0.0599 | -0.062 | -0.1621 | 0.1371 | 163.4666 | 31.0448 | -27.5343 | 14 | 0.0132 | 0.0071 | -0.0109 | 0.0077 | -0.0094 | 0.0175 | -0.0077 | -0.0769 | 0.0164 | 0.0172 | -0.0333 | -0.0044 | 0.0001 | 0.0111 | -0.0299 | 0.1152 | -0.0052 | 0.0048 | 0.192 | -0.0483 | 0.0269 | 179.9845 | 54.4612 | 9.9851 | 15 | 0.0083 | 0.0016 | -0.0006 | 0.0006 | -0.002 | 0.0059 | -0.0004 | -0.0516 | -0.0132 | 0.0146 | -0.0025 | -0.0021 | -0.0089 | -0.0074 | 0.0039 | 0.1425 | -0.0424 | 0.0592 | 0.239 | 0.0058 | 0.0082 | 171.2339 | 46.4097 | 11.4246 | 16 | 0.0144 | 0.0116 | -0.0126 | 0.0049 | -0.0075 | 0.0082 | 0.0055 | -0.1051 | -0.0433 | 0.0428 | -0.0198 | 0.0303 | 0.0215 | -0.0386 | -0.0019 | 0.0586 | -0.0791 | 0.1159 | 0.1817 | 0.0302 | -0.0707 | 164.8712 | 42.923 | 4.5745 | 17 | 0.0012 | -0.0002 | 0.0022 | 0.0007 | -0.0001 | 0.0049 | -0.0049 | -0.004 | 0.0055 | -0.0029 | 0.0004 | 0.0035 | -0.0035 | -0.0088 | -0.0003 | 0.115 | 0.0015 | 0.0404 | 0.1362 | -0.0126 | 0.0442 | 162.4979 | 56.3273 | -5.1007 | 18 | 0.0039 | 0.0039 | -0.001 | 0.0046 | -0.0034 | 0.0155 | -0.0113 | -0.0095 | 0.0017 | 0.0004 | -0.0209 | 0.0039 | -0.0006 | -0.0045 | -0.0293 | 0.0841 | -0.0191 | 0.0277 | 0.1194 | -0.0305 | 0.0059 | 173.875 | 56.0038 | -1.9616 | 19 | 0.0256 | -0.0175 | 0.0046 | 0.0125 | -0.0114 | 0.0319 | -0.0183 | 0.064 | 0.0787 | -0.011 | -0.0421 | -0.0533 | -0.0034 | 0.0095 | -0.0569 | 0.0901 | 0.0345 | 0.0291 | 0.0636 | 0.0925 | 0.1272 | 194.7221 | 68.9674 | -41.1867 | 20 | 0.0125 | -0.0106 | 0.0088 | 0.0092 | -0.0088 | 0.008 | -0.0109 | 0.0335 | 0.0222 | -0.0183 | -0.0313 | -0.0332 | 0.0206 | 0.0099 | -0.0421 | 0.1193 | 0.0586 | 0.1025 | 0.0948 | 0.1388 | 0.1481 | 203.0141 | 62.5253 | -46.8905 | 21 | 0.0251 | 0.0015 | -0.0225 | 0.007 | -0.0053 | 0.0193 | 0.0123 | 0.089 | 0.0913 | -0.0563 | -0.0649 | -0.1903 | 0.0383 | 0.0621 | -0.0348 | 0.0701 | 0.031 | 0.0407 | -0.0119 | 0.1754 | 0.1204 | 207.4806 | 57.97 | -38.8222 | 22 | 0.0036 | 0.0016 | -0.0001 | 0.0017 | 0.0026 | 0.0043 | -0.0128 | -0.0281 | 0.022 | 0.0119 | -0.0134 | 0.0167 | 0.0193 | -0.007 | 0 | 0.1331 | 0.0152 | -0.0049 | 0.0967 | -0.0114 | 0.086 | 200.2588 | 48.8408 | 4.3057 | 23 | 0.0135 | 0.0072 | -0.0073 | 0.0106 | 0.0052 | 0.0128 | -0.0326 | -0.0496 | 0.0719 | 0.0242 | 0.0314 | -0.0001 | -0.0223 | 0.0174 | 0.0107 | 0.1379 | 0.0022 | -0.0525 | 0.0927 | -0.0884 | 0.1225 | 207.0538 | 63.2824 | 5.905 | 24 | 0.0134 | -0.0022 | -0.0033 | 0.0119 | 0.0013 | 0.0224 | -0.0369 | 0.0103 | 0.0874 | 0.006 | 0.03 | -0.0465 | 0.001 | 0.0916 | -0.0009 | 0.0869 | -0.014 | -0.0139 | 0.069 | -0.0125 | 0.0749 | 211.8602 | 55.0373 | -6.6494 | 25 | 0.001 | -0.0015 | 0.0009 | 0.0055 | 0.0026 | 0.0108 | 0.0131 | 0.019 | -0.0433 | 0.014 | 0.0062 | 0.0091 | 0.0236 | -0.0137 | 0.0307 | 0.0871 | -0.0224 | 0.01 | 0.067 | -0.1029 | 0.1034 | 196.4457 | 19.1902 | -29.6196 | 26 | 0.0379 | 0.0037 | -0.0013 | 0.0066 | 0.0045 | 0.0096 | -0.0139 | 0.028 | -0.0861 | 0.0627 | -0.0066 | -0.0402 | 0.0362 | -0.0004 | -0.0235 | 0.0935 | -0.0032 | -0.0062 | -0.023 | -0.0698 | 0.0711 | 208.6909 | 25.8678 | -23.4208 |
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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 20 )A3 - 20 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 21 through 46 )A21 - 46 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 47 through 86 )A47 - 86 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 87 through 111 )A87 - 111 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 112 through 130 )A112 - 130 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 131 through 177 )A131 - 177 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 178 through 227 )A178 - 227 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 228 through 245 )A228 - 245 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 246 through 259 )A246 - 259 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 260 through 297 )A260 - 297 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 3 through 111 )B3 - 111 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 112 through 130 )B112 - 130 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 131 through 297 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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