8G1Y
Crystal Structure of the Threonine Synthase from Streptococcus pneumoniae in complex with Pyridoxal 5-phosphate.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 292 | Protein: 8.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 2mM PLP; Screen: Classics II (B11), 2.1M DL-Malic acid pH 7.0; Cryo: 25% glycerol in screen solution. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.19 | 43.8 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 86.464 | α = 90 |
b = 81.413 | β = 94.6 |
c = 139.465 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Be | 2021-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.9787 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||
1 | 1.43 | 30 | 94.4 | 0.078 | 0.078 | 0.087 | 0.039 | 0.995 | 19.5 | 4.8 | 167626 | -3 | 13.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.43 | 1.45 | 90.6 | 0.853 | 0.853 | 0.96 | 0.434 | 0.792 | 1.9 | 4.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.43 | 29.29 | 159092 | 8365 | 94.3 | 0.1578 | 0.1568 | 0.1769 | RANDOM | 16.724 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.33 | 0.02 | -0.47 | 0.78 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.343 |
r_dihedral_angle_4_deg | 18.413 |
r_dihedral_angle_3_deg | 9.198 |
r_dihedral_angle_1_deg | 4.095 |
r_angle_refined_deg | 1.381 |
r_angle_other_deg | 0.373 |
r_chiral_restr | 0.069 |
r_gen_planes_refined | 0.056 |
r_gen_planes_other | 0.051 |
r_bond_refined_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7592 |
Nucleic Acid Atoms | |
Solvent Atoms | 1113 |
Heterogen Atoms | 99 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |