Software | Name | Classification |
---|
d*TREK | data scalingd*TREK | data reductionCNS | refinementCNS | phasing | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DIX Resolution: 1.5→37.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 315208.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.23 | 3152 | 5.1 % | RANDOM |
---|
Rwork | 0.212 | - | - | - |
---|
all | - | 62367 | - | - |
---|
obs | - | 62367 | 92.5 % | - |
---|
|
---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5283 Å2 / ksol: 0.386094 e/Å3 |
---|
Displacement parameters | Biso mean: 13 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 0.61 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | -1.08 Å2 | 0 Å2 |
---|
3- | - | - | 0.48 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.2 Å | 0.18 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.14 Å | 0.09 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 1.5→37.41 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 3258 | 0 | 48 | 410 | 3716 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_bond_d0.005 | | X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.4 | | X-RAY DIFFRACTION | c_improper_angle_d0.89 | | X-RAY DIFFRACTION | c_mcbond_it1.01 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.49 | 2 | X-RAY DIFFRACTION | c_scbond_it1.91 | 2 | X-RAY DIFFRACTION | c_scangle_it2.77 | 2.5 | | | | | | | | |
|
---|
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.25 | 359 | 5.2 % |
---|
Rwork | 0.244 | 6526 | - |
---|
obs | - | 6885 | 62.2 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER.PARAM | X-RAY DIFFRACTION | 3 | 5GMP_XPLOR.PARAM | | | | |
|
---|
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 37.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 |
---|
Solvent computation | *PLUS |
---|
Displacement parameters | *PLUS |
---|
Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal |
---|
X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg23.4 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.89 | | | | |
|
---|