Software | Name | Version | Classification |
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CrystalClear | | data collectionPHENIX | | model buildingREFMAC | 5.6.0117refinementCrystalClear | | data reductionSCALA | | data scalingPHENIX | | phasing | | | | | | |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.077 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.22833 | 394 | 4.7 % | RANDOM |
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Rwork | 0.18084 | - | - | - |
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obs | 0.18308 | 7974 | 91.27 % | - |
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all | - | 8366 | - | - |
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK |
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Displacement parameters | Biso mean: 22.881 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.4 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.43 Å2 | 0 Å2 |
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3- | - | - | -0.97 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1159 | 0 | 0 | 120 | 1279 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target | Number |
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X-RAY DIFFRACTION | r_bond_refined_d0.017 | 0.019 | 1194 | X-RAY DIFFRACTION | r_angle_refined_deg1.474 | 1.942 | 1619 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.285 | 5 | 155 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.93 | 24.2 | 50 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.631 | 15 | 190 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg10.647 | 15 | 7 | X-RAY DIFFRACTION | r_chiral_restr0.098 | 0.2 | 174 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.021 | 913 | | | | | | | | |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.355 | 24 | - |
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Rwork | 0.18 | 559 | - |
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obs | - | - | 99.49 % |
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Refinement TLS params. | Method: refined / Origin x: 13.5179 Å / Origin y: -0.0255 Å / Origin z: -1.0266 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0313 Å2 | 0.0097 Å2 | -0.0084 Å2 | - | 0.0068 Å2 | -0.007 Å2 | - | - | 0.0338 Å2 |
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L | 1.6544 °2 | 0.0941 °2 | -0.1564 °2 | - | 2.822 °2 | -0.2802 °2 | - | - | 4.5849 °2 |
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S | -0.0195 Å ° | -0.0151 Å ° | -0.1309 Å ° | -0.0185 Å ° | 0.0504 Å ° | -0.0815 Å ° | 0.3669 Å ° | 0.0947 Å ° | -0.0309 Å ° |
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