Software | Name | Classification |
---|
DENZO | data reductionSCALEPACK | data scalingCNS | refinementCNS | phasing | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN ADENOSINE KINASE (PDB 1BX4) Resolution: 1.8→46.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1071084.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.233 | 1641 | 5 % | RANDOM |
---|
Rwork | 0.214 | - | - | - |
---|
obs | 0.214 | 33069 | 97.9 % | - |
---|
all | - | 33069 | - | - |
---|
|
---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.04 Å2 / ksol: 0.369 e/Å3 |
---|
Displacement parameters | Biso mean: 26.8 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 5.37 Å2 | 0 Å2 | 4.64 Å2 |
---|
2- | - | -3.25 Å2 | 0 Å2 |
---|
3- | - | - | -2.12 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.25 Å | 0.22 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.18 Å | 0.16 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 1.8→46.78 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 2605 | 0 | 25 | 142 | 2772 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_bond_d0.005 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.6 | | X-RAY DIFFRACTION | c_improper_angle_d0.78 | | X-RAY DIFFRACTION | c_mcbond_it0.96 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.53 | 2 | X-RAY DIFFRACTION | c_scbond_it1.52 | 2 | X-RAY DIFFRACTION | c_scangle_it2.29 | 2.5 | | | | | | | | |
|
---|
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.293 | 4729 | 5.1 % |
---|
Rwork | 0.273 | 253 | - |
---|
obs | - | - | 88.9 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | PROTEIN_REP.PAPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAWATER.TOPX-RAY DIFFRACTION | 3 | ION.PARAMION.TOPX-RAY DIFFRACTION | 4 | ACY.PARAMACY.TOPX-RAY DIFFRACTION | 5 | DNA-RNA_REP.PA | DNA-RNA_BC.TOP | | | | | | | | |
|
---|
Software | *PLUS Name: CNS / Classification: refinement |
---|
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % |
---|
Solvent computation | *PLUS |
---|
Displacement parameters | *PLUS Biso mean: 26.8 Å2 |
---|
Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg22.6 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.78 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
|
---|
LS refinement shell | *PLUS Rfactor Rfree: 0.293 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.273 / Rfactor obs: 0.273 |
---|