Software | Name | Version | Classification |
---|
XDS | | data reductionXSCALE | | data scalingPHASER | 2.7.17phasingPHENIX | 1.18.2refinementPDB_EXTRACT | 3.25 | data extraction | | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: albicin Resolution: 1.42→31.43 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 17.44 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.1932 | 1598 | 4.89 % |
---|
Rwork | 0.1792 | 31065 | - |
---|
obs | 0.1798 | 32663 | 98.47 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
---|
Displacement parameters | Biso max: 59.27 Å2 / Biso mean: 20.3324 Å2 / Biso min: 6.24 Å2 |
---|
Refinement step | Cycle: final / Resolution: 1.42→31.43 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 970 | 0 | 21 | 222 | 1213 |
---|
Biso mean | - | - | 39.68 | 31.54 | - |
---|
Num. residues | - | - | - | - | 119 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.005 | 1052 | X-RAY DIFFRACTION | f_angle_d0.855 | 1427 | X-RAY DIFFRACTION | f_dihedral_angle_d26.267 | 407 | X-RAY DIFFRACTION | f_chiral_restr0.077 | 157 | X-RAY DIFFRACTION | f_plane_restr0.005 | 178 | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
---|
1.42-1.47 | 0.2375 | 143 | 0.2178 | 2433 | 2576 | 87 | 1.47-1.52 | 0.1945 | 141 | 0.1872 | 2762 | 2903 | 98 | 1.52-1.58 | 0.1933 | 148 | 0.1796 | 2804 | 2952 | 99 | 1.58-1.65 | 0.2102 | 148 | 0.1799 | 2809 | 2957 | 99 | 1.65-1.74 | 0.2225 | 132 | 0.1803 | 2825 | 2957 | 100 | 1.74-1.85 | 0.2179 | 145 | 0.1899 | 2835 | 2980 | 100 | 1.85-1.99 | 0.2036 | 163 | 0.1787 | 2835 | 2998 | 100 | 1.99-2.19 | 0.2004 | 144 | 0.1697 | 2859 | 3003 | 100 | 2.19-2.51 | 0.1766 | 156 | 0.164 | 2883 | 3039 | 100 | 2.51-3.16 | 0.1675 | 134 | 0.1839 | 2932 | 3066 | 100 | 3.16-31.43 | 0.1935 | 144 | 0.1804 | 3088 | 3232 | 100 |
|
---|
Refinement TLS params. | Method: refined / Origin x: 27.3719 Å / Origin y: 0.9709 Å / Origin z: 53.6677 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
---|
T | 0.0865 Å2 | 0.0121 Å2 | -0.0022 Å2 | - | 0.0791 Å2 | 0.0051 Å2 | - | - | 0.0678 Å2 |
---|
L | 0.4778 °2 | 0.4736 °2 | -0.0843 °2 | - | 4.7739 °2 | 0.6918 °2 | - | - | 0.6024 °2 |
---|
S | -0.0176 Å ° | -0.0223 Å ° | -0.041 Å ° | 0.1196 Å ° | 0.0425 Å ° | -0.1155 Å ° | 0.0502 Å ° | -0.0147 Å ° | -0.0174 Å ° |
---|
|
---|
Refinement TLS group | Selection details: (chain 'A' and resid 1 through 119) |
---|