4P52
Crystal structure of homoserine kinase from Cytophaga hutchinsonii ATCC 33406, NYSGRC Target 032717.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.2 | 298 | 0.2M Na2HPO4/KH2PO4, pH 6.2, 2.5M sodium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.13 | 70.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.608 | α = 90 |
b = 101.608 | β = 90 |
c = 195.982 | γ = 120 |
Symmetry | |
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Space Group | P 64 2 2 |
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 | RAYONIX MX225HE | 2014-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9791 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.6 | 50 | 99.9 | 0.141 | 7.4 | 6.3 | 34842 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.64 | 100 | 0.769 | 5.7 | 1730 |
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 | 2.6 | 29.33 | 19067 | 960 | 99.94 | 0.1741 | 0.1723 | 0.209 | RANDOM | 39.363 |
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] | |
0.58 | 0.58 | -1.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.886 |
r_dihedral_angle_4_deg | 19.206 |
r_dihedral_angle_3_deg | 15.236 |
r_dihedral_angle_1_deg | 6.36 |
r_scbond_it | 4.285 |
r_mcangle_it | 3.338 |
r_mcbond_it | 1.97 |
r_angle_refined_deg | 1.474 |
r_chiral_restr | 0.098 |
r_bond_refined_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2329 |
Nucleic Acid Atoms | |
Solvent Atoms | 122 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
SHELX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHENIX | model building |
SHELXD | phasing |