Software | Name | Version | Classification |
---|
CNS | 1.1 | refinementCBASS | | data collectionSCALEPACK | | data scalingCNS | | phasing | | | |
|
---|
Refinement | Method to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.28→20.81 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 450767.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: dna-rna_ums.par
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.2 | 581 | 11 % | RANDOM |
---|
Rwork | 0.177 | - | - | - |
---|
all | 0.182 | 5901 | - | - |
---|
obs | 0.177 | 5275 | 89.3 % | - |
---|
|
---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.2222 Å2 / ksol: 0.3 e/Å3 |
---|
Displacement parameters | Biso mean: 15 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 0.7 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | 0.7 Å2 | 0 Å2 |
---|
3- | - | - | -1.41 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.15 Å | 0.13 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.1 Å | 0.11 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 1.28→20.81 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 0 | 162 | 3 | 44 | 209 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_bond_d0.012 | | X-RAY DIFFRACTION | c_angle_deg1.8 | | X-RAY DIFFRACTION | c_dihedral_angle_d33.1 | | X-RAY DIFFRACTION | c_improper_angle_d2.07 | | X-RAY DIFFRACTION | c_mcbond_it1.23 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.5 | 2 | X-RAY DIFFRACTION | c_scbond_it1.28 | 2 | X-RAY DIFFRACTION | c_scangle_it1.92 | 2.5 | | | | | | | | |
|
---|
LS refinement shell | Resolution: 1.28→1.36 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.231 | 81 | 12.8 % |
---|
Rwork | 0.237 | 552 | - |
---|
obs | - | - | 66.6 % |
---|
|
---|
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 | | | | | | | |
|
---|