Software | Name | Version | Classification |
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PROTEUM2 | | data collectionSAINT | | data reductionSADABS | | data reductionXPREP | | data reductionCNS | | refinementPROTEUM PLUS | 2 | data reductionSAINT | | data scalingSADABS | | data scalingCNS | | phasing | | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A:2trx.pdb Resolution: 2.5→38.69 Å / Rfactor Rfree error: 0.016 / Occupancy max: 1 / Occupancy min: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: XTALVIEW and MOLBROBITY were also used for the refinement.
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.274 | 283 | 5.1 % | random |
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Rwork | 0.223 | - | - | - |
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all | - | 6393 | - | - |
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obs | - | 5499 | 86 % | - |
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 50.8937 Å2 / ksol: 0.324627 e/Å3 |
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Displacement parameters | Biso max: 72.55 Å2 / Biso mean: 23.29 Å2 / Biso min: 1.01 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 11.2 Å2 | -2.5 Å2 | -2.15 Å2 |
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2- | - | -4.83 Å2 | 1.02 Å2 |
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3- | - | - | -6.36 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.41 Å | 0.3 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.6 Å | 0.38 Å |
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Luzzati d res high | - | 2.5 |
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Refinement step | Cycle: LAST / Resolution: 2.5→38.69 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1614 | 0 | 0 | 35 | 1649 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.006 | X-RAY DIFFRACTION | c_angle_deg1.2 | X-RAY DIFFRACTION | c_dihedral_angle_d23.7 | X-RAY DIFFRACTION | c_improper_angle_d0.72 | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | % reflection Rfree (%) | Rfactor Rwork | Num. reflection Rwork | Rfactor Rfree error | Num. reflection all | Num. reflection obs | % reflection obs (%) |
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2.5-2.61 | 0.442 | 33 | 5.3 | 0.31 | 593 | 0.077 | 799 | 626 | 78.3 | 2.61-2.75 | 0.453 | 36 | 5.6 | 0.311 | 610 | 0.076 | 798 | 646 | 81 | 2.75-2.92 | 0.254 | 25 | 3.6 | 0.241 | 663 | 0.051 | 793 | 688 | 86.8 | 2.92-3.15 | 0.291 | 45 | 6.2 | 0.227 | 679 | 0.043 | 800 | 724 | 90.5 | 3.15-3.47 | 0.266 | 41 | 5.6 | 0.232 | 689 | 0.042 | 796 | 730 | 91.7 | 3.47-3.97 | 0.248 | 41 | 5.6 | 0.192 | 691 | 0.039 | 811 | 732 | 90.3 | 3.97-5 | 0.21 | 36 | 5.1 | 0.163 | 665 | 0.035 | 794 | 701 | 88.2 | 5-38.69 | 0.211 | 26 | 4 | 0.232 | 626 | 0.041 | 805 | 652 | 81 |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | protein_rep.paramprotein.topX-RAY DIFFRACTION | 2 | carbohydrate.paramcarbohydrate.topX-RAY DIFFRACTION | 3 | water_rep.paramwater.top | | | | | |
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