1Y9D
Pyruvate Oxidase variant V265A from Lactobacillus plantarum
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
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.11 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 94.66 | ¦Á = 90 |
b = 155.78 | ¦Â = 92.92 |
c = 100.75 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 110 | CCD | MARRESEARCH | 2003-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8123 | EMBL/DESY, HAMBURG | X13 |
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 | 2.2 | 27.3 | 0.062 | 20.6 | 147394 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1POW | 2.2 | 27.3 | 147399 | 139647 | 7369 | 99.69 | 0.18068 | 0.17763 | 0.23794 | RANDOM | 46.443 |
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] | |
0.37 | -0.11 | 2.38 | -2.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.755 |
r_dihedral_angle_4_deg | 19.623 |
r_dihedral_angle_3_deg | 17.462 |
r_dihedral_angle_1_deg | 7.015 |
r_scangle_it | 4.428 |
r_scbond_it | 2.715 |
r_mcangle_it | 1.788 |
r_angle_refined_deg | 1.677 |
r_mcbond_it | 0.971 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17318 |
Nucleic Acid Atoms | |
Solvent Atoms | 1848 |
Heterogen Atoms | 238 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |