6V2N
Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys254Ser
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OEN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 293 | 2 ul drop containing 2 mg/ml Lys254Ser E. coli PCK, 5 mM MnCl2, 5mM MgCl2, 2mM ATP, 2mM pyruvate, 1 mM EDTA, 200 mM ammonium acetate, 100 mM sodium acetate pH 4.8, 0.01 mM DTT and 10% PEG 4000, was added to 2 ul drop containing 0.2 M calcium chloride and 20% PEG. Rod like crystals formed after 7 days, were harvested, and soaked in cryoprotectant solution (30% glycerol, 1mM EDTA, 100 mM sodium acetate, 200 mM ammonium acetate and 12% PEG 4000) for 10 seconds and flash cooled in liquid nitrogen |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.906 | α = 90 |
b = 76.647 | β = 96.38 |
c = 65.421 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 105 | CCD | RAYONIX MX300HE | 2014-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.9793 | CLSI | 08ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.65 | 44.45 | 99.83 | 0.07574 | 0.08409 | 0.03608 | 0.997 | 14.67 | 5.1 | 64733 | 13.82 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.65 | 1.709 | 99.92 | 0.3185 | 0.3562 | 0.1576 | 0.953 | 4.56 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1OEN | 1.65 | 44.29 | 1.38 | 64727 | 1353 | 99.84 | 0.1465 | 0.1459 | 0.1743 | 19.5675 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4025 |
Nucleic Acid Atoms | |
Solvent Atoms | 523 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |