3B8I
Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 18% PEG 3350, 20% glycerol, 0.1M MES, 10 mg/mL protein in 5mM MgCl2, 5mM oxalate, 10mM Na+Hepes pH 7.0; Crystallization drops contained equal volumes of reservoir solution and protein solution, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 260.065 | α = 90 |
b = 83.835 | β = 112.14 |
c = 104.874 | 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | mirrors | 2005-08-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.9 | 47.6 | 97 | 0.054 | 10.9 | 3.27 | 164404 | 159433 |
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 | 1.9 | 1.97 | 77.8 | 0.358 | 2.1 | 2.13 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | THROUGHOUT | 1.9 | 47.6 | 164404 | 143568 | 15857 | 96.97 | 0.19696 | 0.1912 | 0.2487 | RANDOM | 34.15 |
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] | |
-1.78 | -0.65 | 0.21 | 1.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.017 |
r_dihedral_angle_4_deg | 18.305 |
r_dihedral_angle_3_deg | 15.832 |
r_dihedral_angle_1_deg | 10.019 |
r_scangle_it | 3.826 |
r_scbond_it | 2.455 |
r_angle_refined_deg | 1.61 |
r_mcangle_it | 1.587 |
r_mcbond_it | 0.961 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12897 |
Nucleic Acid Atoms | |
Solvent Atoms | 1859 |
Heterogen Atoms | 90 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
CrystalClear | data reduction |
CrystalClear | data scaling |
MLPHARE | phasing |