Software | Name | Version | Classification |
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JBluIce-EPICS | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.8_1069)refinementXDS | | data reductionXDS | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→29.793 Å / SU ML: 0.31 / σ(F): 2 / Phase error: 29.06 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.253 | 1994 | 3.19 % |
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Rwork | 0.2041 | - | - |
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obs | 0.2057 | 62598 | 99.44 % |
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all | - | 66216 | - |
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 2.45→29.793 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10543 | 0 | 60 | 171 | 10774 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 10848 | X-RAY DIFFRACTION | f_angle_d0.609 | 14646 | X-RAY DIFFRACTION | f_dihedral_angle_d11.717 | 3961 | X-RAY DIFFRACTION | f_chiral_restr0.039 | 1578 | X-RAY DIFFRACTION | f_plane_restr0.002 | 1838 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.45-2.5113 | 0.3361 | 133 | 0.2788 | 4273 | X-RAY DIFFRACTION | 100 | 2.5113-2.5791 | 0.334 | 148 | 0.2632 | 4292 | X-RAY DIFFRACTION | 100 | 2.5791-2.655 | 0.3254 | 141 | 0.2538 | 4284 | X-RAY DIFFRACTION | 99 | 2.655-2.7406 | 0.2973 | 144 | 0.2475 | 4296 | X-RAY DIFFRACTION | 100 | 2.7406-2.8385 | 0.3284 | 140 | 0.2423 | 4334 | X-RAY DIFFRACTION | 100 | 2.8385-2.952 | 0.3346 | 142 | 0.2313 | 4337 | X-RAY DIFFRACTION | 100 | 2.952-3.0862 | 0.2832 | 138 | 0.243 | 4290 | X-RAY DIFFRACTION | 100 | 3.0862-3.2488 | 0.3077 | 146 | 0.2347 | 4323 | X-RAY DIFFRACTION | 100 | 3.2488-3.452 | 0.3035 | 149 | 0.2295 | 4343 | X-RAY DIFFRACTION | 100 | 3.452-3.7181 | 0.248 | 139 | 0.2097 | 4347 | X-RAY DIFFRACTION | 100 | 3.7181-4.0914 | 0.2649 | 138 | 0.1852 | 4379 | X-RAY DIFFRACTION | 100 | 4.0914-4.6815 | 0.1873 | 144 | 0.1598 | 4357 | X-RAY DIFFRACTION | 100 | 4.6815-5.8907 | 0.1995 | 147 | 0.1669 | 4419 | X-RAY DIFFRACTION | 100 | 5.8907-29.7955 | 0.2355 | 145 | 0.2091 | 4330 | X-RAY DIFFRACTION | 95 |
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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 | 2.454 | 0.2404 | 0.5835 | 1.334 | -0.196 | 6.7704 | -0.1291 | -0.004 | 0.1794 | -0.0275 | 0.0652 | -0.1228 | -0.152 | 0.4551 | 0.0856 | 0.2872 | -0.0253 | -0.0075 | 0.4081 | 0.0203 | 0.4725 | -72.4105 | 65.8693 | -240.3809 | 2 | 4.8581 | -1.7081 | -2.616 | 4.206 | 1.1504 | 3.9001 | -0.0214 | 0.0379 | 0.0213 | 0.1165 | 0.1927 | -0.3026 | 0.0949 | 0.3304 | -0.1505 | 0.3395 | 0.0327 | -0.0216 | 0.6212 | -0.1302 | 0.4319 | -39.3804 | 76.8254 | -207.058 | 3 | 1.5601 | 1.3961 | 0.3918 | 2.7285 | 1.2114 | 1.6563 | 0.0396 | 0.0729 | 0.014 | 0.026 | -0.0514 | -0.0104 | -0.0753 | -0.0021 | -0.0196 | 0.2063 | 0.2128 | 0.0105 | 0.3196 | 0.0726 | 0.234 | -69.5696 | 71.8006 | -195.7141 | 4 | 1.4449 | 0.8253 | -0.4266 | 2.5735 | 0.832 | 1.5604 | 0.1941 | -0.3884 | -0.0759 | 0.6715 | -0.2338 | -0.0759 | 0.2628 | 0.0185 | 0.0963 | 0.4241 | 0.3513 | -0.1096 | 0.6565 | 0.2997 | 0.2923 | -83.0854 | 71.3071 | -163.5929 | 5 | 0.2399 | 0.7648 | 0.3414 | 1.0452 | 0.9018 | 0.7177 | 0.11 | -0.0211 | 0.0947 | 0.1606 | -0.0928 | 0.1843 | -0.0227 | -0.1372 | -0.0262 | 0.483 | 0.1453 | 0.0014 | 0.4442 | -0.0149 | 0.4907 | -79.7043 | 72.7849 | -191.7568 | 6 | 0.5406 | 0.8284 | 0.0674 | 2.0294 | 0.8408 | 0.8821 | 0.0406 | -0.1823 | 0.1754 | 0.0801 | -0.2102 | 0.437 | -0.0766 | -0.1272 | 0.1529 | 0.6237 | 0.1497 | 0.0595 | 0.8037 | 0.006 | 0.6815 | -87.9716 | 75.0809 | -165.3676 |
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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 B AND RESID 9:283 )B9 - 283 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 10:281 )A10 - 281 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN M AND RESID 1:108 ) OR ( CHAIN L AND RESID 1:108 )M1 - 108 | 4 | X-RAY DIFFRACTION | 3 | ( CHAIN M AND RESID 1:108 ) OR ( CHAIN L AND RESID 1:108 )L1 - 108 | 5 | X-RAY DIFFRACTION | 4 | ( CHAIN M AND RESID 109:200 ) OR ( CHAIN L AND RESID 109:210 )M109 - 200 | 6 | X-RAY DIFFRACTION | 4 | ( CHAIN M AND RESID 109:200 ) OR ( CHAIN L AND RESID 109:210 )L109 - 210 | 7 | X-RAY DIFFRACTION | 5 | ( CHAIN I AND RESID 1:114 ) OR ( CHAIN H AND RESID 1:114 )I1 - 114 | 8 | X-RAY DIFFRACTION | 5 | ( CHAIN I AND RESID 1:114 ) OR ( CHAIN H AND RESID 1:114 )H1 - 114 | 9 | X-RAY DIFFRACTION | 6 | ( CHAIN I AND RESID 115:212 ) OR ( CHAIN H AND RESID 115:212 | | | | | | | | | | | | | | | | |
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