4KGD
High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4FEE | PDB ENTRY 4FEE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 280 | 1.5 M ammonium sulfate, 200 mM phosphate, 0.1 mM thiamine diphosphate, 1 mM magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.28 | α = 90 |
b = 154.16 | β = 90 |
c = 165.47 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 315r | Toroidal focusing mirror | 2011-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.979200 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.06 | 35 | 94.9 | 0.07 | 0.081 | 9.68 | 3.38 | 645341 | 645341 | -3 | 10.593 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.06 | 1.13 | 93.2 | 0.52 | 2.21 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | FOURIER SYNTHESIS | FREE R | PDB ENTRY 4FEE | 1.06 | 30 | 625966 | 645341 | 19361 | 91.6 | 0.1271 | 0.1271 | 0.1505 | RANDOM | 12.8418 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
285 | 8946.42 | 11037.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_angle_d | 310 |
s_zero_chiral_vol | 79 |
s_non_zero_chiral_vol | 6 |
s_approx_iso_adps | 0.105 |
s_anti_bump_dis_restr | 0.087 |
s_similar_adp_cmpnt | 0.046 |
s_from_restr_planes | 0.037 |
s_bond_d | 0.015 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9048 |
Nucleic Acid Atoms | |
Solvent Atoms | 1899 |
Heterogen Atoms | 225 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
SHELX | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |
PHENIX | phasing |
SHELXL | refinement |