Software | Name | Version | Classification |
---|
DENZO | | data reductionSCALA | | data scalingAMoRE | | phasingCNS | 1 | refinement CCP4 | (SCALA)data scaling | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: VHH52 anti-R1 unliganded Resolution: 1.95→18.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2310814.65 / 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 | 0.266 | 1194 | 8 % | RANDOM |
---|
Rwork | 0.232 | - | - | - |
---|
obs | 0.232 | 15003 | 99.3 % | - |
---|
all | - | 0 | - | - |
---|
|
---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.87 Å2 / ksol: 0.364 e/Å3 |
---|
Displacement parameters | Biso mean: 32.2 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 5.94 Å2 | 5.75 Å2 | 0 Å2 |
---|
2- | - | 5.94 Å2 | 0 Å2 |
---|
3- | - | - | -11.87 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.32 Å | 0.27 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.27 Å | 0.23 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 1.95→18.5 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 977 | 0 | 45 | 164 | 1186 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_bond_d0.007 | | X-RAY DIFFRACTION | c_angle_deg1.5 | | X-RAY DIFFRACTION | c_dihedral_angle_d24.6 | | X-RAY DIFFRACTION | c_improper_angle_d0.71 | | X-RAY DIFFRACTION | c_mcbond_it1.24 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.11 | 2 | X-RAY DIFFRACTION | c_scbond_it1.67 | 2 | X-RAY DIFFRACTION | c_scangle_it2.38 | 2.5 | | | | | | | | |
|
---|
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.305 | 133 | 9.2 % |
---|
Rwork | 0.29 | 1319 | - |
---|
obs | - | 0 | 54.4 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | RR1_240399.PARAMRR1_240399.TOPX-RAY DIFFRACTION | 4 | SO4.PARAMSO4.TOP | | | | | | | |
|
---|
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
---|
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8 % |
---|
Solvent computation | *PLUS |
---|
Displacement parameters | *PLUS Biso mean: 32.2 Å2 |
---|
Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_angle_deg1.5 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg24.6 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.71 | | 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: 0.305 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.29 |
---|