Software | Name | Version | Classification |
---|
XDS | | data reductionPHENIX | (phenix.refine: 1.7_650)refinement Coot | | model buildingXSCALE | | data scaling | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BJ7 Resolution: 1.75→38.48 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.08 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.2315 | 1595 | 5 % | Random |
---|
Rwork | 0.2109 | 30295 | - | - |
---|
obs | 0.2119 | 31890 | 99.1 % | - |
---|
|
---|
Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.509 Å2 / ksol: 0.375 e/Å3 |
---|
Displacement parameters | Biso max: 95.58 Å2 / Biso mean: 38.0664 Å2 / Biso min: 24.25 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 8.5473 Å2 | 0 Å2 | -0 Å2 |
---|
2- | - | 8.5473 Å2 | 0 Å2 |
---|
3- | - | - | -17.0946 Å2 |
---|
|
---|
Refinement step | Cycle: final / Resolution: 1.75→38.48 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 1217 | 0 | 0 | 90 | 1307 |
---|
Biso mean | - | - | - | 45.29 | - |
---|
Num. residues | - | - | - | - | 151 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.006 | 1277 | X-RAY DIFFRACTION | f_angle_d0.978 | 1736 | X-RAY DIFFRACTION | f_chiral_restr0.076 | 193 | X-RAY DIFFRACTION | f_plane_restr0.004 | 229 | X-RAY DIFFRACTION | f_dihedral_angle_d13.473 | 500 | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
---|
1.7501-1.8065 | 0.3737 | 141 | 0.3975 | 2680 | 2821 | 98 | 1.8065-1.8711 | 0.3164 | 143 | 0.3278 | 2708 | 2851 | 99 | 1.8711-1.946 | 0.3355 | 142 | 0.2922 | 2724 | 2866 | 99 | 1.946-2.0346 | 0.2725 | 143 | 0.2278 | 2697 | 2840 | 98 | 2.0346-2.1418 | 0.2522 | 143 | 0.2042 | 2732 | 2875 | 99 | 2.1418-2.276 | 0.2853 | 145 | 0.218 | 2742 | 2887 | 99 | 2.276-2.4517 | 0.2573 | 144 | 0.2145 | 2746 | 2890 | 99 | 2.4517-2.6984 | 0.2181 | 147 | 0.2327 | 2789 | 2936 | 100 | 2.6984-3.0887 | 0.2639 | 145 | 0.2394 | 2749 | 2894 | 99 | 3.0887-3.8909 | 0.2189 | 148 | 0.1968 | 2805 | 2953 | 99 | 3.8909-38.4892 | 0.1948 | 154 | 0.1808 | 2923 | 3077 | 99 |
|
---|