Software | Name | Classification |
---|
CNS | refinementDENZO | data reductionSCALEPACK | data scalingCNS | phasing | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GID Resolution: 2.8→38.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 561769.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.293 | 1670 | 5 % | RANDOM |
---|
Rwork | 0.29 | - | - | - |
---|
all | 0.29 | 38092 | - | - |
---|
obs | 0.29 | 33255 | 87.3 % | - |
---|
|
---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 79.5611 Å2 / ksol: 0.318679 e/Å3 |
---|
Displacement parameters | Biso mean: 122.8 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -42.06 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | 84.76 Å2 | 0 Å2 |
---|
3- | - | - | -42.7 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.53 Å | 0.56 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.91 Å | 1.17 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 2.8→38.72 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 0 | 6714 | 10 | 236 | 6960 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal |
---|
X-RAY DIFFRACTION | c_bond_d0.006 | X-RAY DIFFRACTION | c_angle_deg1.2 | X-RAY DIFFRACTION | c_dihedral_angle_d15 | X-RAY DIFFRACTION | c_improper_angle_d1.48 | | | | |
|
---|
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.521 | 198 | 4.9 % |
---|
Rwork | 0.5497 | 3877 | - |
---|
obs | - | - | 65.2 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | DNA-RNA_REP.PARAM | DNA-RNA.TOP | X-RAY DIFFRACTION | 2 | WATER_REP.PARAM | X-RAY DIFFRACTION | 3 | ION.PARAM | | |
|
---|
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 99 Å / Rfactor all: 0.29 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.29 |
---|
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_deg15 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg1.48 | | | | |
|
---|
LS refinement shell | *PLUS Rfactor Rfree: 0.521 / Rfactor Rwork: 0.549 |
---|