Software | Name | Version | Classification |
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MD2 | diffractometer software from EMBL (with LS-CAT developed extensions) | data collection CCP4 | | model buildingMOLREP | | phasingREFMAC | 5.5.0109refinementHKL-2000 | | data reductionHKL-2000 | | data scaling CCP4 | | phasing | | | | | | | |
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Refinement | Method to determine structure : MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EY2 Resolution: 1.24→31.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.361 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.044 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection | Selection details |
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Rfree![](img/lk-wikipe.gif) | 0.20723 | 776 | 5 % | RANDOM |
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Rwork![](img/lk-wikipe.gif) | 0.15941 | - | - | - |
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obs | 0.16169 | 14841 | 98.17 % | - |
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all | - | 15944 | - | - |
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK |
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Displacement parameters | Biso mean: 18.337 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.61 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -1.03 Å2 | 0 Å2 |
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3- | - | - | -0.58 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.24→31.45 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 410 | 0 | 80 | 490 |
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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_d0.036 | 0.021 | 454 | X-RAY DIFFRACTION | r_angle_refined_deg2.608 | 3 | 688 | X-RAY DIFFRACTION | r_chiral_restr0.411 | 0.2 | 82 | X-RAY DIFFRACTION | r_gen_planes_refined0.035 | 0.02 | 210 | X-RAY DIFFRACTION | r_scbond_it3.11 | 3 | 454 | X-RAY DIFFRACTION | r_scangle_it3.896 | 4.5 | 688 | X-RAY DIFFRACTION | r_rigid_bond_restr2.778 | 3 | 454 | | | | | | | |
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LS refinement shell | Resolution: 1.24→1.273 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.25 | 57 | - |
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Rwork | 0.205 | 959 | - |
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obs | - | - | 88.12 % |
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