Software | Name | Version | Classification |
---|
CBASS | | data collectionPHASES | | phasingREFMAC | 5.2.0019refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DNS Resolution: 1.38→30.32 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.592 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.19414 | 216 | 4.7 % | RANDOM |
---|
Rwork | 0.17838 | - | - | - |
---|
all | 0.17907 | 4650 | - | - |
---|
obs | - | 4373 | 94.04 % | - |
---|
|
---|
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK |
---|
Displacement parameters | Biso mean: 12.133 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | 0.12 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | 0.12 Å2 | 0 Å2 |
---|
3- | - | - | -0.24 Å2 |
---|
|
---|
Refine analyze | | Free | Obs |
---|
Luzzati coordinate error | 0.06 Å | 0.061 Å |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 1.38→30.32 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 0 | 163 | 1 | 38 | 202 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target | Number |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.007 | 0.021 | 180 | X-RAY DIFFRACTION | r_angle_refined_deg1.467 | 3 | 270 | X-RAY DIFFRACTION | r_chiral_restr0.057 | 0.2 | 31 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 83 | X-RAY DIFFRACTION | r_nbd_refined0.371 | 0.2 | 66 | X-RAY DIFFRACTION | r_nbtor_refined0.277 | 0.2 | 103 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.102 | 0.2 | 29 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.18 | 0.2 | 26 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.083 | 0.2 | 10 | X-RAY DIFFRACTION | r_scbond_it0.825 | 3 | 261 | X-RAY DIFFRACTION | r_scangle_it1.249 | 4.5 | 270 | | | | | | | | | | | |
|
---|
LS refinement shell | Resolution: 1.38→1.416 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.157 | 14 | - |
---|
Rwork | 0.203 | 216 | - |
---|
obs | - | - | 65.53 % |
---|
|
---|
Refinement TLS params. | Method: refined / Origin x: 31.5133 Å / Origin y: 30.4882 Å / Origin z: 2.3842 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
---|
T | 0.0169 Å2 | -0.0065 Å2 | 0.0054 Å2 | - | -0.0057 Å2 | -0.0025 Å2 | - | - | 0.0077 Å2 |
---|
L | 0.1824 °2 | -0.3805 °2 | -0.0034 °2 | - | 1.305 °2 | 0.2072 °2 | - | - | 0.2928 °2 |
---|
S | -0.0049 Å ° | 0.0122 Å ° | 0.0094 Å ° | 0.1295 Å ° | 0.0189 Å ° | -0.0139 Å ° | 0.0248 Å ° | -0.0403 Å ° | -0.014 Å ° |
---|
|
---|