2PXZ
E. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ATP, Mg2+, Mn2+, carbon dioxide and oxaloacetate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.4 | 294 | 8ul drop with 8ug/ml protein, 2mM ADP, 5mM MgCl2, 10 uM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate and 12% w/v PEG 4000 was allowed to equilibrate with a 1 ml reservoir of 100 mM sodium aceate, 200 mM ammonium acetate and 27% PEG 4000. After crystals grew for one week 2ul of a 1 mM EDTA and saturated sodium oxaloacetate solution was added to the drop. 5 ul of glycerol was added to the drop. A 0.1 x 0.1 x 0.3 mm crystal was removed with a loop and flash cooled in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.556 | α = 90 |
b = 94.302 | β = 95.54 |
c = 46.354 | 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 | MARMOSAIC 225 mm CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 1.3317 | CLSI | 08ID-1 |
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 | 1.83 | 47.14 | 100 | 0.085 | 3.6 | 595228 | 171743 | 13.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.23 | 2.28 | 100 | 2.5 | 3.5 | 24303 |
Refinement
Statistics | |||||||||||||||||||
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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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.23 | 38.32 | 24889 | 1322 | 100 | 0.17585 | 0.17277 | 0.23421 | RANDOM | 20.323 |
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] | |
0.02 | 0.01 | -0.04 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.049 |
r_dihedral_angle_4_deg | 16.591 |
r_dihedral_angle_3_deg | 15.914 |
r_dihedral_angle_1_deg | 7.025 |
r_scangle_it | 4.049 |
r_scbond_it | 2.767 |
r_angle_refined_deg | 1.932 |
r_mcangle_it | 1.653 |
r_mcbond_it | 1.047 |
r_symmetry_hbond_refined | 0.374 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4007 |
Nucleic Acid Atoms | |
Solvent Atoms | 283 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |