Software | Name | Version | Classification |
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HKL-2000 | | data collectionMOLREP | | phasingPHENIX | (phenix.refine)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z3E Resolution: 1.9→36.318 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU ML: 0.29 / σ(F): 0.1 / Phase error: 19.89 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2317 | 1000 | 10.18 % |
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Rwork | 0.1864 | 8828 | - |
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obs | 0.1909 | 9828 | 97.37 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.454 Å2 / ksol: 0.377 e/Å3 |
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Displacement parameters | Biso max: 86.04 Å2 / Biso mean: 33.022 Å2 / Biso min: 13.37 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.068 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 8.912 Å2 | 0 Å2 |
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3- | - | - | -7.844 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.9→36.318 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 934 | 0 | 0 | 46 | 980 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 972 | X-RAY DIFFRACTION | f_angle_d0.813 | 1317 | X-RAY DIFFRACTION | f_dihedral_angle_d15.555 | 375 | X-RAY DIFFRACTION | f_chiral_restr0.056 | 155 | X-RAY DIFFRACTION | f_plane_restr0.003 | 171 | | | | | |
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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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1.9-2.0002 | 0.2877 | 139 | 0.1923 | 1158 | X-RAY DIFFRACTION | 93 | 2.0002-2.1255 | 0.2404 | 133 | 0.1643 | 1217 | X-RAY DIFFRACTION | 96 | 2.1255-2.2896 | 0.2018 | 142 | 0.1603 | 1235 | X-RAY DIFFRACTION | 96 | 2.2896-2.5199 | 0.2366 | 140 | 0.1719 | 1255 | X-RAY DIFFRACTION | 98 | 2.5199-2.8844 | 0.2461 | 140 | 0.2062 | 1283 | X-RAY DIFFRACTION | 99 | 2.8844-3.6335 | 0.2634 | 151 | 0.1883 | 1300 | X-RAY DIFFRACTION | 99 | 3.6335-36.3251 | 0.202 | 155 | 0.1858 | 1380 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: -1.834 Å / Origin y: -5.784 Å / Origin z: 3.793 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1273 Å2 | -0.0021 Å2 | -0.0081 Å2 | - | 0.1431 Å2 | 0.0053 Å2 | - | - | 0.1188 Å2 |
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L | 0.6367 °2 | -0.301 °2 | 0.198 °2 | - | 0.6599 °2 | 0.0859 °2 | - | - | -0.0203 °2 |
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S | -0.0925 Å ° | -0.0775 Å ° | -0.0351 Å ° | 0.059 Å ° | 0.0459 Å ° | 0.0214 Å ° | -0.0929 Å ° | 0.0332 Å ° | 0.0306 Å ° |
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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 | allA1 - 117 | 2 | X-RAY DIFFRACTION | 1 | allA1 - 167 | | | | |
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