Software | Name | Version | Classification |
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PHENIX | (phenix.refine: 1.8.2_1309)refinementXDS | | data reductionXDS | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GLP Resolution: 2.302→20 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.49 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.191 | 1414 | 100 % |
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Rwork | 0.191 | - | - |
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obs | 0.191 | 1414 | 96.98 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 2.302→20 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 187 | 0 | 8 | 195 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 208 | X-RAY DIFFRACTION | f_angle_d1.783 | 322 | X-RAY DIFFRACTION | f_dihedral_angle_d12.473 | 99 | X-RAY DIFFRACTION | f_chiral_restr0.069 | 43 | X-RAY DIFFRACTION | f_plane_restr0.01 | 9 | | | | | |
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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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2.3023-2.3846 | 0.2601 | 110 | 0.2601 | 110 | X-RAY DIFFRACTION | 80 | 2.3846-2.48 | 0.2437 | 128 | 0.2437 | 128 | X-RAY DIFFRACTION | 96 | 2.48-2.5928 | 0.2532 | 142 | 0.2532 | 142 | X-RAY DIFFRACTION | 99 | 2.5928-2.7293 | 0.3011 | 133 | 0.3011 | 133 | X-RAY DIFFRACTION | 99 | 2.7293-2.9001 | 0.2879 | 147 | 0.2879 | 147 | X-RAY DIFFRACTION | 99 | 2.9001-3.1237 | 0.2736 | 139 | 0.2736 | 139 | X-RAY DIFFRACTION | 99 | 3.1237-3.4374 | 0.1901 | 140 | 0.1901 | 140 | X-RAY DIFFRACTION | 97 | 3.4374-3.9333 | 0.1825 | 143 | 0.1825 | 143 | X-RAY DIFFRACTION | 100 | 3.9333-4.95 | 0.1262 | 154 | 0.1262 | 154 | X-RAY DIFFRACTION | 99 | 4.95-26.0327 | 0.1565 | 178 | 0.1565 | 178 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: refined / Origin x: 7.6478 Å / Origin y: 4.2841 Å / Origin z: 4.6019 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.3682 Å2 | 0.0128 Å2 | 0.019 Å2 | - | 0.4807 Å2 | 0.0308 Å2 | - | - | 0.4485 Å2 |
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L | 0.1075 °2 | -0.0414 °2 | 0.0534 °2 | - | 0.0467 °2 | -0.0187 °2 | - | - | 0.0272 °2 |
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S | -0.0057 Å ° | 0.2064 Å ° | 0.3664 Å ° | 0.0758 Å ° | -0.1573 Å ° | -0.1933 Å ° | -0.111 Å ° | 0.4647 Å ° | 0.0002 Å ° |
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Refinement TLS group | Selection: all / Selection details: chain B |
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