Software | Name | Version | Classification |
---|
CNS | 1.1 | refinementCBASS | | data collectionDENZO | | data reductionSCALEPACK | | data scalingCNS | | phasing | | | | |
|
---|
Refinement | Method to determine structure : MOLECULAR REPLACEMENT Starting model: pdb entry 1Z7I Resolution: 1.4→18.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 711051.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: DNA-RNA
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection | Selection details |
---|
Rfree![](img/lk-wikipe.gif) | 0.187 | 435 | 10.2 % | RANDOM |
---|
Rwork![](img/lk-wikipe.gif) | 0.17 | - | - | - |
---|
all![](img/lk-wikipe.gif) | 0.172 | 4252 | - | - |
---|
obs | 0.17 | 4252 | 92.8 % | - |
---|
|
---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.0525 Å2 / ksol: 0.34 e/Å3 |
---|
Displacement parameters | Biso mean: 18.5 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.86 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | -0.86 Å2 | 0 Å2 |
---|
3- | - | - | 1.71 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.15 Å | 0.13 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.08 Å | 0.08 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 1.4→18.72 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 0 | 163 | 0 | 43 | 206 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal |
---|
X-RAY DIFFRACTION | c_bond_d0.015 | X-RAY DIFFRACTION | c_angle_deg1.9 | X-RAY DIFFRACTION | c_dihedral_angle_d34.3 | X-RAY DIFFRACTION | c_improper_angle_d2.04 | | | | |
|
---|
LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.244 | 52 | 9.6 % |
---|
Rwork | 0.221 | 492 | - |
---|
obs | - | 492 | 73.7 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | protein_rep.paramprotein.topX-RAY DIFFRACTION | 2 | water_rep.paramdna-rna.top | X-RAY DIFFRACTION | 3 | ion.paramwater.topX-RAY DIFFRACTION | 4 | dna-rna_ums.par | ion.topX-RAY DIFFRACTION | 5 | cac.parums.top | | | | | | | |
|
---|