2PY7
Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AYL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 293 | A 2ul drop with 4 mg/ml protein, 20 mM Tris-HCl (pH 7.6), 0.5 mM EDTA, 5 mM ADP, 2.5 mM phosphoenolpyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 0.1 M sodium acetate, 0.05 M sodium cacodylate (pH 6.5), 15% PEG 8000 was allowed to equilibrate with a 1 ml well of 0.2 M sodium aceate, 0.1 M sodium cacodylate 30% PEG 8000. After a week a 0.1 x 0.1 x 0.4 mm crystal was removed and put in a small volume of well solution with 30% glycerol added. The crystal was put into a loop and flash cooled in liquid notrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.999 | α = 90 |
b = 95.663 | β = 96.12 |
c = 46.319 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | CCD | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.919 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.02 | 99 | 85.95 | 0.1 | 2.95 | 89783 | 36560 | 13.96 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.02 | 2.28 | 59.6 | 0.14 | 4.9 | 1.17 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1AYL | 2.2 | 18.48 | 24587 | 1282 | 94.1 | 0.15795 | 0.15484 | 0.21792 | RANDOM | 14.325 |
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] | |
0.02 | -0.03 | 0.04 | -0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.833 |
r_dihedral_angle_4_deg | 16.456 |
r_dihedral_angle_3_deg | 13.948 |
r_dihedral_angle_1_deg | 5.684 |
r_scangle_it | 2.205 |
r_scbond_it | 1.372 |
r_angle_refined_deg | 1.234 |
r_mcangle_it | 0.869 |
r_mcbond_it | 0.523 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4133 |
Nucleic Acid Atoms | |
Solvent Atoms | 570 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |