Software | Name | Version | Classification |
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PHENIX | 1.11.1_2575refinementAimless | 0.5.27data scalingPHASER | 2.7.16phasingPDB_EXTRACT | 3.24 | data extractionMOSFLM | | data reduction | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BJP Resolution: 2.721→38.266 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.59
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.259 | 369 | 10.17 % |
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Rwork | 0.2481 | - | - |
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obs | 0.2494 | 3629 | 98.43 % |
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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: 185.23 Å2 / Biso mean: 111.852 Å2 / Biso min: 55.75 Å2 |
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Refinement step | Cycle: final / Resolution: 2.721→38.266 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 785 | 41 | 0 | 826 |
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Biso mean | - | - | 67.75 | - | - |
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Num. residues | - | - | - | - | 36 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 924 | X-RAY DIFFRACTION | f_angle_d1.224 | 1438 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 180 | X-RAY DIFFRACTION | f_plane_restr0.007 | 42 | X-RAY DIFFRACTION | f_dihedral_angle_d21.1 | 433 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.7208-3.1143 | 0.3798 | 117 | 0.3375 | 1081 | 1198 | 99 | 3.1143-3.9231 | 0.3393 | 129 | 0.275 | 1059 | 1188 | 98 | 3.9231-38.2697 | 0.2196 | 123 | 0.226 | 1120 | 1243 | 99 |
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Refinement TLS params. | Method: refined / Origin x: 1.9361 Å / Origin y: 50.9448 Å / Origin z: 20.1079 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.4202 Å2 | 0.7988 Å2 | -0.0171 Å2 | - | 2.1706 Å2 | -0.1022 Å2 | - | - | 0.9266 Å2 |
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L | 0.2479 °2 | 0.0454 °2 | 0.0931 °2 | - | 0.0047 °2 | 0.0561 °2 | - | - | 0.0839 °2 |
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S | -0.1008 Å ° | 0.5513 Å ° | 0.1966 Å ° | -0.0584 Å ° | 0.4011 Å ° | 0.1721 Å ° | -0.6301 Å ° | -2.1287 Å ° | -0.0534 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 - 36 | 2 | X-RAY DIFFRACTION | 1 | allC1 | 3 | X-RAY DIFFRACTION | 1 | allD1 | | | | | | |
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