Software | Name | Version | Classification |
---|
DENZO | | data reductionxia2 | | data scalingPHASER | | phasingSHARP | | phasingRESOLVE | | phasingREFMAC | 5.8.0189refinementPDB_EXTRACT | 3.24 | data extraction | | | | | | | |
|
---|
Refinement | Method to determine structure: SAD / Resolution: 1.25→45.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.007 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.034 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.1646 | 1877 | 5 % | RANDOM |
---|
Rwork | 0.1621 | - | - | - |
---|
obs | 0.1623 | 35666 | 99.94 % | - |
---|
|
---|
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å |
---|
Displacement parameters | Biso max: 61.55 Å2 / Biso mean: 21.854 Å2 / Biso min: 11.76 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.59 Å2 | 0 Å2 | 0 Å2 |
---|
2- | - | -0.59 Å2 | 0 Å2 |
---|
3- | - | - | 1.17 Å2 |
---|
|
---|
Refinement step | Cycle: final / Resolution: 1.25→45.97 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 809 | 0 | 36 | 93 | 938 |
---|
Biso mean | - | - | 34.38 | 30.54 | - |
---|
Num. residues | - | - | - | - | 104 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target | Number |
---|
X-RAY DIFFRACTION | r_bond_refined_d0.005 | 0.019 | 871 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 736 | X-RAY DIFFRACTION | r_angle_refined_deg1.164 | 1.988 | 1186 | X-RAY DIFFRACTION | r_angle_other_deg1.047 | 3 | 1727 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.539 | 5 | 105 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg40.317 | 24.39 | 41 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.49 | 15 | 138 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg12.278 | 15 | 6 | X-RAY DIFFRACTION | r_chiral_restr0.067 | 0.2 | 133 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.021 | 950 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 167 | X-RAY DIFFRACTION | r_rigid_bond_restr0.802 | 3 | 1607 | X-RAY DIFFRACTION | r_sphericity_free16.274 | 5 | 56 | X-RAY DIFFRACTION | r_sphericity_bonded8.614 | 5 | 1624 | | | | | | | | | | | | | | |
|
---|
LS refinement shell | Resolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.2 | 134 | - |
---|
Rwork | 0.174 | 2576 | - |
---|
all | - | 2710 | - |
---|
obs | - | - | 100 % |
---|
|
---|
Refinement TLS params. | Method: refined / Origin x: 24.1599 Å / Origin y: 52.6364 Å / Origin z: 24.9349 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
---|
T | 0.0019 Å2 | 0.0002 Å2 | 0.0013 Å2 | - | 0.0009 Å2 | -0.0002 Å2 | - | - | 0.002 Å2 |
---|
L | 0.2959 °2 | 0.0517 °2 | 0.1918 °2 | - | 0.1806 °2 | 0.01 °2 | - | - | 0.1369 °2 |
---|
S | 0.0032 Å ° | 0.0024 Å ° | 0.006 Å ° | 0.0006 Å ° | -0.0039 Å ° | 0.0008 Å ° | 0.0012 Å ° | 0.0042 Å ° | 0.0007 Å ° |
---|
|
---|