Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingX-PLOR | | model buildingCNS | 1 | refinementX-PLOR | | phasing | | | | |
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Refinement | Method to determine structure: 1JZE / Resolution: 1.7→22.88 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2147551.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.277 | 941 | 8.1 % | RANDOM |
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Rwork | 0.269 | - | - | - |
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all | - | 12712 | - | - |
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obs | - | 12712 | 98 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.4102 Å2 / ksol: 0.370202 e/Å3 |
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Displacement parameters | Biso mean: 35 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 9.97 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -10.8 Å2 | 0 Å2 |
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3- | - | - | 0.82 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.34 Å | 0.31 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.37 Å | 0.31 Å |
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Refinement step | Cycle: LAST / Resolution: 1.7→22.88 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 974 | 0 | 33 | 86 | 1093 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.01 | | X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d24.9 | | X-RAY DIFFRACTION | c_improper_angle_d1.08 | | X-RAY DIFFRACTION | c_mcbond_it0.2 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it0.38 | 2 | X-RAY DIFFRACTION | c_scbond_it0.14 | 2 | X-RAY DIFFRACTION | c_scangle_it0.2 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.38 | 67 | 8.2 % |
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Rwork | 0.334 | 753 | - |
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obs | - | - | 91.2 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | PARAM19X.HEMEWATER.TOPX-RAY DIFFRACTION | 3 | TPY.PARTPY.TOPX-RAY DIFFRACTION | 4 | WATER.PARAMTOPH19X.HEME | | | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 8.1 % / Rfactor obs: 0.269 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 35 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg24.9 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg1.08 | | X-RAY DIFFRACTION | c_mcbond_it0.2 | 1.5 | X-RAY DIFFRACTION | c_scbond_it0.14 | 2 | X-RAY DIFFRACTION | c_mcangle_it0.38 | 2 | X-RAY DIFFRACTION | c_scangle_it0.2 | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.38 / % reflection Rfree: 8.2 % / Rfactor Rwork: 0.334 |
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