Software | Name | Version | Classification |
---|
CBASS | | data collectionSHELX | | model buildingSHARP | | phasingWARP | | model buildingCNS | 1.1 | refinementHKL-2000 | | data reductionHKL-2000 | | data scalingSHELX | | phasing | | | | | | | |
|
---|
Refinement | Method to determine structure: SAD / Resolution: 2.3→43.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 76406.44 / 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 | 0.269 | 3520 | 4 % | RANDOM |
---|
Rwork | 0.217 | - | - | - |
---|
all | 0.24 | 91961 | - | - |
---|
obs | 0.217 | 87765 | 95.4 % | - |
---|
|
---|
Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.4019 Å2 / ksol: 0.329415 e/Å3 |
---|
Displacement parameters | Biso mean: 25.8 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 2.73 Å2 | 0 Å2 | 2.61 Å2 |
---|
2- | - | -4.21 Å2 | 0 Å2 |
---|
3- | - | - | 1.48 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.36 Å | 0.29 Å |
---|
Luzzati d res low | - | 5 Å |
---|
Luzzati sigma a | 0.37 Å | 0.29 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 2.3→43.1 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 13839 | 0 | 8 | 620 | 14467 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
---|
X-RAY DIFFRACTION | c_bond_d0.007 | | X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d24.1 | | X-RAY DIFFRACTION | c_improper_angle_d0.91 | | X-RAY DIFFRACTION | c_mcbond_it1.24 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.01 | 2 | X-RAY DIFFRACTION | c_scbond_it1.94 | 2 | X-RAY DIFFRACTION | c_scangle_it2.71 | 2.5 | | | | | | | | |
|
---|
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.341 | 552 | 4.1 % |
---|
Rwork | 0.275 | 12990 | - |
---|
obs | - | - | 88.6 % |
---|
|
---|
Xplor file | Refine-ID | Serial no | Param file | Topol file |
---|
X-RAY DIFFRACTION | 1 | protein_rep.paramprotein.topX-RAY DIFFRACTION | 2 | dna-rna_rep.param | dna-rna.top | X-RAY DIFFRACTION | 3 | water_rep.paramwater.topX-RAY DIFFRACTION | 4 | ion.paramion.top | | | | | |
|
---|