Software | Name | Version | Classification |
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PHENIX | dev_2443refinementPDB_EXTRACT | 3.22 | data extractionXDS | | data reductionXDS | | data scalingPHASER | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.711→51.603 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.84
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2322 | 1493 | 4.87 % |
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Rwork | 0.2047 | - | - |
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obs | 0.206 | 30671 | 98.44 % |
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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: 121.64 Å2 / Biso mean: 34.5841 Å2 / Biso min: 16.57 Å2 |
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Refinement step | Cycle: final / Resolution: 1.711→51.603 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2063 | 0 | 111 | 184 | 2358 |
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Biso mean | - | - | 69.55 | 39.72 | - |
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Num. residues | - | - | - | - | 266 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 2340 | X-RAY DIFFRACTION | f_angle_d0.739 | 3184 | X-RAY DIFFRACTION | f_chiral_restr0.052 | 348 | X-RAY DIFFRACTION | f_plane_restr0.004 | 420 | X-RAY DIFFRACTION | f_dihedral_angle_d15.29 | 1465 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.7107-1.7659 | 0.3764 | 152 | 0.353 | 2560 | 2712 | 98 | 1.7659-1.829 | 0.3122 | 143 | 0.3375 | 2591 | 2734 | 98 | 1.829-1.9022 | 0.3221 | 124 | 0.3182 | 2647 | 2771 | 99 | 1.9022-1.9888 | 0.2735 | 133 | 0.2769 | 2616 | 2749 | 99 | 1.9888-2.0937 | 0.3091 | 126 | 0.2215 | 2645 | 2771 | 99 | 2.0937-2.2249 | 0.2318 | 136 | 0.2089 | 2640 | 2776 | 99 | 2.2249-2.3966 | 0.2157 | 119 | 0.1997 | 2643 | 2762 | 99 | 2.3966-2.6378 | 0.2088 | 129 | 0.2019 | 2693 | 2822 | 100 | 2.6378-3.0195 | 0.2179 | 160 | 0.2026 | 2669 | 2829 | 99 | 3.0195-3.804 | 0.2276 | 128 | 0.1709 | 2689 | 2817 | 97 | 3.804-51.6267 | 0.1933 | 143 | 0.1692 | 2785 | 2928 | 97 |
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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 | 7.4126 | 4.9657 | 2.9945 | 5.9979 | -0.0833 | 7.022 | 0.2579 | -0.1637 | -0.2244 | -0.024 | -0.104 | -0.0003 | 0.6636 | 0.1814 | -0.085 | 0.2789 | 0.0426 | 0.0072 | 0.1619 | -0.0552 | 0.2494 | 13.6081 | 11.4429 | 17.6515 | 2 | 2.1313 | -4.2242 | 6.0327 | 5.8521 | -1.4911 | 8.2611 | 0.3568 | 0.0917 | -0.4628 | -0.6478 | -0.1892 | 0.3957 | 0.1591 | -0.0655 | -0.1776 | 0.2588 | -0.0483 | -0.0248 | 0.1918 | 0.0348 | 0.2587 | 5.6745 | 18.4514 | 3.5793 | 3 | 1.1247 | 0.2052 | 0.2426 | 2.923 | -0.8712 | 5.1054 | 0.0042 | 0.0166 | 0.134 | 0.0683 | 0.096 | 0.1818 | -0.4138 | -0.2065 | -0.0827 | 0.2361 | -0.013 | 0.0455 | 0.1814 | -0.0053 | 0.2033 | 5.6955 | 26.2362 | 15.6873 | 4 | 5.0802 | -0.3391 | 2.1089 | 4.1777 | 0.427 | 3.5168 | 0.1641 | -0.0314 | -0.0617 | -0.1589 | -0.0676 | -0.1734 | 0.0624 | 0.1778 | -0.0628 | 0.2198 | -0.0656 | 0.039 | 0.1994 | 0.0092 | 0.2102 | 15.1457 | 23.0244 | 9.0252 | 5 | 0.281 | -0.3991 | -1.8653 | 1.0614 | 4.7951 | 2.0136 | 0.1217 | -0.0093 | -0.0253 | -0.0844 | -0.0226 | 0.0141 | -1.0496 | 0.0651 | -0.1114 | 0.3516 | -0.0731 | 0.0351 | 0.2799 | -0.0086 | 0.2222 | 16.6524 | 28.3001 | 9.1258 | 6 | 2.3036 | -1.315 | -1.4086 | 5.9527 | -1.2481 | 1.8958 | -0.1951 | -0.089 | -0.0959 | 0.6885 | 0.2345 | -0.346 | -0.1358 | 0.3813 | -0.0893 | 0.2704 | -0.0103 | -0.0092 | 0.2188 | -0.0128 | 0.1771 | 11.9844 | 17.7529 | 21.1952 | 7 | 2.0388 | -7.1609 | 2.804 | 9.71 | -2.4101 | 7.3991 | -0.008 | 0.4081 | -0.0831 | 0.0401 | 0.1095 | 0.4205 | 0.1391 | 0.322 | 0.0605 | 0.2922 | -0.0307 | -0.0143 | 0.1872 | -0.0005 | 0.2984 | 11.054 | 12.0706 | 6.8397 | 8 | 5.6527 | 2.1582 | 2.4841 | 4.4885 | 4.7537 | 8.1604 | 0.1845 | 0.0425 | 0.2488 | 0.1965 | -0.1097 | -0.1095 | -0.085 | -0.0576 | -0.0977 | 0.2295 | -0.0292 | -0.0198 | 0.1344 | 0.031 | 0.2139 | 4.6081 | 2.8668 | 10.8967 | 9 | 4.2254 | 0.5679 | -1.0444 | 3.8543 | -0.9674 | 2.4026 | -0.0106 | -0.2685 | 0.0408 | 0.3053 | -0.0061 | -0.3744 | 0.0156 | 0.2179 | 0.0043 | 0.2077 | 0.0047 | -0.0368 | 0.1809 | -0.0366 | 0.165 | 13.1964 | -5.536 | 14.7666 | 10 | 9.1935 | 1.2359 | -2.5116 | 2.0247 | 0.9209 | 8.0178 | 0.2337 | -0.9867 | -0.0629 | 1.1018 | 0.0951 | -0.7539 | 0.5443 | 0.1234 | -0.2402 | 0.3625 | 0.047 | -0.0827 | 0.3316 | 0.0315 | 0.3143 | 21.8313 | -16.7536 | 18.7783 | 11 | 9.6644 | -1.7148 | -5.4162 | 2.1047 | 0.9916 | 3.5261 | -0.2518 | -0.2305 | -0.3911 | 0.2599 | 0.0266 | 0.1231 | 0.3433 | 0.1249 | 0.214 | 0.2757 | 0.0034 | 0.0155 | 0.1968 | 0.0058 | 0.1928 | 8.4082 | -15.7807 | 15.8046 | 12 | 4.5932 | 1.7998 | 2.3444 | 4.9936 | -0.7534 | 4.1439 | -0.4329 | 0.1243 | 0.7707 | -0.0901 | 0.0276 | -1.2096 | -0.0521 | 0.34 | 0.3769 | 0.2115 | 0.0388 | -0.022 | 0.2492 | -0.0385 | 0.385 | 21.3244 | -6.6638 | 7.4622 | 13 | 8.9495 | -0.2394 | 1.8466 | 9.3235 | 0.327 | 5.9637 | -0.0703 | 0.3943 | -0.1142 | -0.5667 | 0.0857 | 0.2544 | 0.2666 | -0.285 | -0.0376 | 0.2291 | -0.014 | -0.0043 | 0.1927 | -0.0032 | 0.1533 | 4.1237 | -9.2442 | 2.9747 | 14 | 2.8306 | -0.2986 | -1.569 | 2.5171 | -0.0147 | 2.1107 | -0.0792 | 0.2179 | -0.1407 | -0.1163 | 0.0418 | 0.0885 | 0.1893 | -0.1579 | 0.0132 | 0.1747 | -0.024 | -0.0249 | 0.1496 | -0.0082 | 0.108 | 5.4099 | -9.854 | 6.7206 | 15 | 9.5515 | -0.3793 | 0.494 | 6.9146 | -2.842 | 3.5207 | 0.1416 | -0.0961 | 0.1216 | 0.1045 | 0.0223 | -0.2681 | 0.2595 | 0.2974 | -0.1136 | 0.222 | 0.0014 | -0.0129 | 0.1469 | -0.0752 | 0.174 | 14.3074 | 1.6922 | 11.9497 |
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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 2 through 15 )A2 - 15 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 17 through 29 )A17 - 29 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 30 through 76 )A30 - 76 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 77 through 99 )A77 - 99 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 100 through 109 )A100 - 109 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 110 through 124 )A110 - 124 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 125 through 134 )A125 - 134 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 2 through 15 )B2 - 15 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 17 through 48 )B17 - 48 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 49 through 56 )B49 - 56 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 57 through 76 )B57 - 76 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 77 through 89 )B77 - 89 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 90 through 99 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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