2EZ8
Pyruvate oxidase variant F479W in complex with reaction intermediate 2-lactyl-thiamin diphosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1POW | pdb entry 1POW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | hanging drop | 5.7 | 280 | ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 56.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.133 | α = 90 |
b = 154.462 | β = 90 |
c = 165.656 | 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 | IMAGE PLATE | MAR scanner 345 mm plate | 2005-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
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 | 1.97 | 24.96 | 98.2 | 0.107 | 11.49 | 4.5 | 105614 | 105590 | 2 | 3.7 | 12.8 |
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 | 1.97 | 2 | 0.871 | 87.1 | 0.275 | 3.5 | 3.7 |
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 (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1POW | 1.963 | 24.96 | 2 | 105614 | 105590 | 2105 | 97.964 | 0.149 | 0.149 | 0.1486 | 0.1722 | RANDOM | 13.078 |
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] | |
1.953 | -1.008 | -0.945 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.135 |
r_dihedral_angle_4_deg | 19.193 |
r_dihedral_angle_3_deg | 13.47 |
r_dihedral_angle_1_deg | 6.155 |
r_scangle_it | 3.715 |
r_scbond_it | 2.22 |
r_angle_refined_deg | 1.463 |
r_mcangle_it | 1.153 |
r_mcbond_it | 0.611 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9046 |
Nucleic Acid Atoms | |
Solvent Atoms | 993 |
Heterogen Atoms | 186 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOLREP | phasing |