Software | Name | Version | Classification |
---|
CNS | 1.3 | refinementXSCALE | | data scalingPDB_EXTRACT | 3.15 | data extraction | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AY3 Resolution: 1.7→26 Å / FOM work R set: 0.8766 / Cross valid method: FREE R-VALUE / σ(F): 0
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.1956 | 745 | 10.9 % |
---|
Rwork | 0.1601 | 6086 | - |
---|
obs | - | 6831 | 99.6 % |
---|
|
---|
Solvent computation | Bsol: 36.2882 Å2 |
---|
Displacement parameters | Biso max: 58.96 Å2 / Biso mean: 18.972 Å2 / Biso min: 9.2 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 1.208 Å2 | 0 Å2 | -2.485 Å2 |
---|
2- | - | -1.831 Å2 | 0 Å2 |
---|
3- | - | - | 0.622 Å2 |
---|
|
---|
Refinement step | Cycle: final / Resolution: 1.7→26 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 0 | 500 | 1 | 158 | 659 |
---|
Biso mean | - | - | 22.38 | 31.88 | - |
---|
Num. residues | - | - | - | - | 24 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_bond_d0.003 | | X-RAY DIFFRACTION | c_angle_d0.839 | | X-RAY DIFFRACTION | c_mcbond_it0 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.393 | 2 | X-RAY DIFFRACTION | c_mcangle_it0 | 2 | X-RAY DIFFRACTION | c_scangle_it1.838 | 2.5 | | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
---|
1.7-1.76 | 0.2062 | 70 | 0.195 | 584 | 654 | 96.3 | 1.76-1.83 | 0.2388 | 61 | 0.2094 | 607 | 668 | 100 | 1.83-1.91 | 0.2662 | 85 | 0.2036 | 601 | 686 | 100 | 1.91-2.02 | 0.2653 | 77 | 0.2041 | 609 | 686 | 100 | 2.02-2.14 | 0.1992 | 81 | 0.1843 | 594 | 675 | 100 | 2.14-2.31 | 0.2374 | 71 | 0.1766 | 615 | 686 | 100 | 2.31-2.54 | 0.2001 | 73 | 0.1678 | 612 | 685 | 100 | 2.54-2.91 | 0.1889 | 74 | 0.1532 | 620 | 694 | 100 | 2.91-3.66 | 0.1732 | 78 | 0.1389 | 607 | 685 | 99.9 | 3.66-26 | 0.1464 | 75 | 0.1263 | 637 | 712 | 99.9 |
|
---|
Xplor file | Refine-ID | Serial no | Param file |
---|
X-RAY DIFFRACTION | 1 | bru.paramX-RAY DIFFRACTION | 2 | dna-rna_free.param | X-RAY DIFFRACTION | 3 | CNS_TOPPAR:water_rep.paramX-RAY DIFFRACTION | 4 | CNS_TOPPAR:ion.param | | |
|
---|